diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index ec72920e3..67674d713 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -33,7 +33,7 @@ Do not worry about migrations either client side or backend unless specifically
 
 ## Libraries
 
-Use Zod for schema and input validation.
+Use Zod for schema and input validation (backend).
 Use Drizzle ORM for database interactions and migrations.
 Use Better-Auth for authentication and user management.
 Use Zag.js for UI components and design system.
diff --git a/.vscode/mcp.json b/.vscode/mcp.json
index 1b492ed87..9bb5d566b 100644
--- a/.vscode/mcp.json
+++ b/.vscode/mcp.json
@@ -4,10 +4,10 @@
       "type": "stdio",
       "command": "node",
       "args": ["${workspaceFolder}/packages/mcp/server.js"]
-    },
-    "stripe": {
-      "type": "http",
-      "url": "https://mcp.stripe.com"
     }
+    // "stripe": {
+    //   "type": "http",
+    //   "url": "https://mcp.stripe.com"
+    // }
   }
 }
diff --git a/packages/mcp/server.js b/packages/mcp/server.js
index efece5d7e..601557736 100644
--- a/packages/mcp/server.js
+++ b/packages/mcp/server.js
@@ -42,7 +42,7 @@ registerCodeReviewTools(server, repoRoot);
 async function main() {
   const transport = new StdioServerTransport();
   await server.connect(transport);
-  console.error('Corates MCP Server started');
+  console.log('Corates MCP Server started');
 }
 
 main().catch(err => {
diff --git a/packages/mcp/tools/lint.js b/packages/mcp/tools/lint.js
index efacf632b..a5f917476 100644
--- a/packages/mcp/tools/lint.js
+++ b/packages/mcp/tools/lint.js
@@ -12,7 +12,7 @@ export function registerLintTools(server, repoRoot) {
       fix: z.boolean().optional().default(false).describe('Whether to run lint with --fix'),
     },
     async ({ fix = false }) => {
-      const command = `pnpm run lint${fix ? ' -- --fix' : ''}`;
+      const command = `pnpm run lint${fix ? ' --fix' : ''}`;
 
       try {
         const { stdout, stderr } = await exec(command, {
diff --git a/packages/ui/src/zag/Collapsible.jsx b/packages/ui/src/zag/Collapsible.jsx
index 4337cd74b..5b2772996 100644
--- a/packages/ui/src/zag/Collapsible.jsx
+++ b/packages/ui/src/zag/Collapsible.jsx
@@ -13,17 +13,15 @@ import { createMemo, createUniqueId } from 'solid-js';
  * @param {JSX.Element} props.children - The content to show/hide
  */
 export default function Collapsible(props) {
-  const open = () => props.open;
-  const defaultOpen = () => props.defaultOpen;
-  const disabled = () => props.disabled;
-  const trigger = () => props.trigger;
-  const children = () => props.children;
-
   const service = useMachine(collapsible.machine, () => ({
     id: createUniqueId(),
-    open: open(),
-    defaultOpen: defaultOpen(),
-    disabled: disabled(),
+    get open() {
+      return props.open;
+    },
+    defaultOpen: props.defaultOpen,
+    get disabled() {
+      return props.disabled;
+    },
     onOpenChange(details) {
       props.onOpenChange?.(details.open);
     },
@@ -33,34 +31,30 @@ export default function Collapsible(props) {
 
   return (
     <div {...api().getRootProps()}>
-      {trigger()?.(api())}
+      {props.trigger?.(api())}
       <div {...api().getContentProps()} class='collapsible-content overflow-hidden'>
-        {children()}
+        {props.children}
       </div>
       <style>{`
         .collapsible-content[data-state="open"] {
-          animation: collapsible-slideDown 200ms ease-out;
+          animation: collapsible-slideDown 150ms ease-out;
         }
         .collapsible-content[data-state="closed"] {
-          animation: collapsible-slideUp 200ms ease-out;
+          animation: collapsible-slideUp 150ms ease-out;
         }
         @keyframes collapsible-slideDown {
           from {
-            opacity: 0;
             height: 0;
           }
           to {
-            opacity: 1;
             height: var(--height);
           }
         }
         @keyframes collapsible-slideUp {
           from {
-            opacity: 1;
             height: var(--height);
           }
           to {
-            opacity: 0;
             height: 0;
           }
         }
diff --git a/packages/web/src/components/checklist-ui/AMSTAR2Checklist.jsx b/packages/web/src/components/checklist-ui/AMSTAR2Checklist.jsx
index e1eae86b9..6f0a449c7 100644
--- a/packages/web/src/components/checklist-ui/AMSTAR2Checklist.jsx
+++ b/packages/web/src/components/checklist-ui/AMSTAR2Checklist.jsx
@@ -3,6 +3,7 @@ import { AMSTAR_CHECKLIST } from '@/AMSTAR2/checklist-map.js';
 import { createChecklist as createAMSTAR2Checklist } from '@/AMSTAR2/checklist.js';
 import { FaSolidCircleInfo } from 'solid-icons/fa';
 import { Tooltip, FloatingPanel } from '@corates/ui';
+import NoteEditor from '@checklist-ui/common/NoteEditor.jsx';
 
 export function Question1(props) {
   const state = () => props.checklistState().q1;
@@ -329,6 +330,12 @@ export function Question9(props) {
     }, 10);
   }
 
+  // Get Y.Text for the note (q9 is parent key for q9a/q9b)
+  const noteYText = () => {
+    if (!props.getQuestionNote) return null;
+    return props.getQuestionNote('q9');
+  };
+
   let containerRef;
 
   return (
@@ -352,6 +359,9 @@ export function Question9(props) {
         columns={question.columns2}
         handleChange={handleChangeB}
       />
+      <Show when={props.getQuestionNote}>
+        <NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
+      </Show>
     </div>
   );
 }
@@ -447,6 +457,12 @@ export function Question11(props) {
     }, 10);
   }
 
+  // Get Y.Text for the note (q11 is parent key for q11a/q11b)
+  const noteYText = () => {
+    if (!props.getQuestionNote) return null;
+    return props.getQuestionNote('q11');
+  };
+
   let containerRef;
 
   return (
@@ -473,6 +489,9 @@ export function Question11(props) {
         handleChange={handleChangeB}
         width='w-48'
       />
+      <Show when={props.getQuestionNote}>
+        <NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
+      </Show>
     </div>
   );
 }
@@ -646,14 +665,31 @@ export function Question16(props) {
 function StandardQuestion(props) {
   let containerRef;
 
+  // Get the question key from the question text (e.g., "1. Did..." -> "q1")
+  const questionKey = () => {
+    const text = props.question?.text || '';
+    const match = text.match(/^(\d+[a-z]?)\./);
+    return match ? `q${match[1]}` : null;
+  };
+
+  // Get Y.Text for the note if getQuestionNote is available
+  const noteYText = () => {
+    const key = questionKey();
+    if (!key || !props.getQuestionNote) return null;
+    return props.getQuestionNote(key);
+  };
+
   return (
-    <div class='bg-white rounded-lg shadow-md p-7 relative' ref={el => (containerRef = el)}>
+    <div class='bg-white rounded-lg shadow-md p-7 pb-3 relative' ref={el => (containerRef = el)}>
       <QuestionInfo question={props.question} containerRef={containerRef} />
       <div class='flex'>
         <h3 class='font-semibold text-sm text-gray-900 mb-1'>{props.question.text}</h3>
         <CriticalButton state={props.state} onUpdate={props.onUpdate} />
       </div>
       <StandardQuestionInternal columns={props.question.columns} {...props} />
+      <Show when={props.getQuestionNote}>
+        <NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
+      </Show>
     </div>
   );
 }
@@ -828,68 +864,100 @@ export default function AMSTAR2Checklist(props = {}) {
               <Question1
                 onUpdate={newQ1 => handleChecklistChange({ q1: newQ1 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question2
                 onUpdate={newQ2 => handleChecklistChange({ q2: newQ2 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question3
                 onUpdate={newQ3 => handleChecklistChange({ q3: newQ3 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question4
                 onUpdate={newQ4 => handleChecklistChange({ q4: newQ4 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question5
                 onUpdate={newQ5 => handleChecklistChange({ q5: newQ5 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question6
                 onUpdate={newQ6 => handleChecklistChange({ q6: newQ6 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question7
                 onUpdate={newQ7 => handleChecklistChange({ q7: newQ7 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question8
                 onUpdate={newQ8 => handleChecklistChange({ q8: newQ8 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question9
                 onUpdatea={newQ9a => handleChecklistChange({ q9a: newQ9a })}
                 onUpdateb={newQ9b => handleChecklistChange({ q9b: newQ9b })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question10
                 onUpdate={newQ10 => handleChecklistChange({ q10: newQ10 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question11
                 onUpdatea={newQ11a => handleChecklistChange({ q11a: newQ11a })}
                 onUpdateb={newQ11b => handleChecklistChange({ q11b: newQ11b })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question12
                 onUpdate={newQ12 => handleChecklistChange({ q12: newQ12 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question13
                 onUpdate={newQ13 => handleChecklistChange({ q13: newQ13 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question14
                 onUpdate={newQ14 => handleChecklistChange({ q14: newQ14 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question15
                 onUpdate={newQ15 => handleChecklistChange({ q15: newQ15 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
               <Question16
                 onUpdate={newQ16 => handleChecklistChange({ q16: newQ16 })}
                 checklistState={currentChecklist}
+                getQuestionNote={props.getQuestionNote}
+                readOnly={props.readOnly}
               />
             </div>
           </fieldset>
diff --git a/packages/web/src/components/checklist-ui/ChecklistWithPdf.jsx b/packages/web/src/components/checklist-ui/ChecklistWithPdf.jsx
index da706078c..5932390fb 100644
--- a/packages/web/src/components/checklist-ui/ChecklistWithPdf.jsx
+++ b/packages/web/src/components/checklist-ui/ChecklistWithPdf.jsx
@@ -23,6 +23,7 @@ export default function ChecklistWithPdf(props) {
   // props.pdfs - array of PDFs for multi-PDF selection
   // props.selectedPdfId - currently selected PDF ID
   // props.onPdfSelect - handler for PDF selection change
+  // props.getQuestionNote - function to get Y.Text for a question note
 
   return (
     <div class='h-full flex flex-col bg-blue-50'>
@@ -39,6 +40,7 @@ export default function ChecklistWithPdf(props) {
           checklist={props.checklist}
           onUpdate={props.onUpdate}
           readOnly={props.readOnly}
+          getQuestionNote={props.getQuestionNote}
         />
 
         {/* Second panel: PDF Viewer */}
diff --git a/packages/web/src/components/checklist-ui/ChecklistYjsWrapper.jsx b/packages/web/src/components/checklist-ui/ChecklistYjsWrapper.jsx
index bad12aa18..62fe1fec1 100644
--- a/packages/web/src/components/checklist-ui/ChecklistYjsWrapper.jsx
+++ b/packages/web/src/components/checklist-ui/ChecklistYjsWrapper.jsx
@@ -23,9 +23,13 @@ export default function ChecklistYjsWrapper() {
   const [selectedPdfId, setSelectedPdfId] = createSignal(null);
 
   // Use full hook for write operations
-  const { updateChecklistAnswer, updateChecklist, getChecklistData, addPdfToStudy } = useProject(
-    params.projectId,
-  );
+  const {
+    updateChecklistAnswer,
+    updateChecklist,
+    getChecklistData,
+    addPdfToStudy,
+    getQuestionNote,
+  } = useProject(params.projectId);
 
   // Read data directly from store for faster reactivity
   const connectionState = () => projectStore.getConnectionState(params.projectId);
@@ -362,6 +366,9 @@ export default function ChecklistYjsWrapper() {
           pdfs={studyPdfs()}
           selectedPdfId={selectedPdfId()}
           onPdfSelect={handlePdfSelect}
+          getQuestionNote={questionKey =>
+            getQuestionNote(params.studyId, params.checklistId, questionKey)
+          }
         />
       </Show>
     </>
diff --git a/packages/web/src/components/checklist-ui/GenericChecklist.jsx b/packages/web/src/components/checklist-ui/GenericChecklist.jsx
index 2399697c4..eae1d5a63 100644
--- a/packages/web/src/components/checklist-ui/GenericChecklist.jsx
+++ b/packages/web/src/components/checklist-ui/GenericChecklist.jsx
@@ -24,6 +24,7 @@ import { ROBINSIChecklist } from '@checklist-ui/ROBINSIChecklist/index.js';
  * @param {Object} props.checklist - The checklist state data
  * @param {Function} props.onUpdate - Callback for checklist updates
  * @param {boolean} [props.readOnly] - Whether the checklist is read-only
+ * @param {Function} [props.getQuestionNote] - Function to get Y.Text for a question note
  */
 export default function GenericChecklist(props) {
   // Determine the checklist type from props or state
@@ -44,6 +45,7 @@ export default function GenericChecklist(props) {
           externalChecklist={props.checklist}
           onExternalUpdate={props.onUpdate}
           readOnly={props.readOnly}
+          getQuestionNote={props.getQuestionNote}
         />
       </Show>
       <Show when={checklistType() === CHECKLIST_TYPES.ROBINS_I}>
diff --git a/packages/web/src/components/checklist-ui/common/NoteEditor.jsx b/packages/web/src/components/checklist-ui/common/NoteEditor.jsx
new file mode 100644
index 000000000..9392f6e28
--- /dev/null
+++ b/packages/web/src/components/checklist-ui/common/NoteEditor.jsx
@@ -0,0 +1,161 @@
+/**
+ * NoteEditor - Y.Text-bound textarea for editing notes
+ *
+ * This component binds directly to a Y.Text instance for real-time
+ * collaborative editing. Changes sync automatically via Yjs.
+ */
+import { createSignal, createEffect, onCleanup, Show } from 'solid-js';
+import { BiRegularChevronRight } from 'solid-icons/bi';
+import { BsJournalText } from 'solid-icons/bs';
+import { Collapsible } from '@corates/ui';
+
+const MAX_HEIGHT = 300;
+
+/**
+ * @param {Object} props
+ * @param {Y.Text} props.yText - The Y.Text instance to bind to
+ * @param {string} [props.placeholder] - Placeholder text
+ * @param {boolean} [props.readOnly] - Whether the editor is read-only
+ * @param {boolean} [props.collapsed] - Start collapsed (default: true)
+ * @param {number} [props.maxLength] - Maximum character limit (default: 2000)
+ * @param {string} [props.label] - Label for the collapsible section
+ */
+export default function NoteEditor(props) {
+  // Initialize expanded state - default to collapsed unless props.collapsed is false
+  // eslint-disable-next-line solid/reactivity -- intentionally read once for initial state
+  const [expanded, setExpanded] = createSignal(!props.collapsed);
+  const [localValue, setLocalValue] = createSignal('');
+  let textareaRef;
+
+  // Initialize from Y.Text and set up observer
+  createEffect(() => {
+    const yText = props.yText;
+    if (!yText) {
+      setLocalValue('');
+      return;
+    }
+
+    // Get initial value
+    setLocalValue(yText.toString());
+
+    // Observe changes from other users
+    const observer = () => {
+      setLocalValue(yText.toString());
+    };
+
+    yText.observe(observer);
+
+    onCleanup(() => {
+      yText.unobserve(observer);
+    });
+  });
+
+  // Handle local input
+  function handleInput(e) {
+    const newValue = e.target.value;
+    const maxLength = props.maxLength ?? 2000;
+
+    // Enforce max length
+    if (newValue.length > maxLength) {
+      e.target.value = newValue.slice(0, maxLength);
+      return;
+    }
+
+    // Immediate resize for snappier feel
+    e.target.style.height = 'auto';
+    e.target.style.height = `${Math.min(e.target.scrollHeight, MAX_HEIGHT)}px`;
+
+    const yText = props.yText;
+    if (!yText || props.readOnly) return;
+
+    // Update Y.Text - delete all and insert new content in a transaction
+    // to avoid intermediate empty states that cause UI flickering
+    yText.doc.transact(() => {
+      yText.delete(0, yText.length);
+      yText.insert(0, newValue);
+    });
+  }
+
+  // Auto-resize textarea as content changes
+  createEffect(() => {
+    const isExpanded = expanded();
+    if (textareaRef && isExpanded) {
+      // Reset height to auto to get correct scrollHeight
+      textareaRef.style.height = 'auto';
+      // Set height to scrollHeight, capped at MAX_HEIGHT
+      textareaRef.style.height = `${Math.min(textareaRef.scrollHeight, MAX_HEIGHT)}px`;
+    }
+  });
+
+  const hasContent = () => localValue().trim().length > 0;
+  const charCount = () => localValue().length;
+  const maxLength = () => props.maxLength ?? 2000;
+
+  return (
+    <div class='mt-3 border-t border-gray-100 pt-2'>
+      <Collapsible
+        open={expanded()}
+        onOpenChange={setExpanded}
+        trigger={api => (
+          <div
+            {...api.getTriggerProps()}
+            class={`
+              flex items-center gap-1.5 py-1 text-xs cursor-pointer select-none
+              ${hasContent() ? 'text-blue-600 hover:text-blue-700' : 'text-gray-500 hover:text-gray-700'}
+            `}
+          >
+            <BiRegularChevronRight
+              class={`w-4 h-4 shrink-0 transition-transform duration-200 ${expanded() ? 'rotate-90' : ''}`}
+            />
+            <BsJournalText class='w-3 h-3 shrink-0' />
+            <span class='font-medium'>{props.label || 'Notes'}</span>
+          </div>
+        )}
+      >
+        <div class='pt-2 px-0.5 pb-0.5'>
+          <textarea
+            ref={textareaRef}
+            value={localValue()}
+            onInput={handleInput}
+            placeholder={props.placeholder || 'Add a note for this question...'}
+            disabled={props.readOnly || !props.yText}
+            class={`
+              w-full px-3 py-2 text-sm border rounded-lg resize-none overflow-hidden
+              focus:outline-none focus:ring-2 focus:ring-blue-500 focus:border-transparent
+              ${props.readOnly ? 'bg-gray-50 text-gray-600 cursor-not-allowed' : 'bg-white text-gray-900'}
+              ${!props.yText ? 'bg-gray-100 cursor-not-allowed' : ''}
+            `}
+            style={{ 'min-height': '60px' }}
+            maxLength={maxLength()}
+          />
+          <div class='flex justify-between items-center mt-1 text-2xs text-gray-400'>
+            <span>{props.readOnly ? 'Read-only' : ''}</span>
+            <span class={charCount() > maxLength() * 0.9 ? 'text-amber-500' : ''}>
+              {charCount()} / {maxLength()}
+            </span>
+          </div>
+        </div>
+      </Collapsible>
+    </div>
+  );
+}
+
+/**
+ * Read-only note display for reconciliation view
+ * Shows the note content without editing capabilities
+ */
+export function NoteDisplay(props) {
+  const hasContent = () => (props.content || '').trim().length > 0;
+
+  return (
+    <Show when={hasContent()}>
+      <div class='mt-2 p-2 bg-gray-50 rounded-lg border border-gray-100'>
+        <div class='flex items-center gap-1.5 text-xs text-gray-500 mb-1'>
+          <BsJournalText class='w-3 h-3' />
+          <span>Notes</span>
+        </div>
+        <p class='text-sm text-gray-700 whitespace-pre-wrap'>{props.content}</p>
+      </div>
+    </Show>
+  );
+}
diff --git a/packages/web/src/components/checklist-ui/compare/ChecklistReconciliation.jsx b/packages/web/src/components/checklist-ui/compare/ChecklistReconciliation.jsx
index 6e74d0846..66eae107f 100644
--- a/packages/web/src/components/checklist-ui/compare/ChecklistReconciliation.jsx
+++ b/packages/web/src/components/checklist-ui/compare/ChecklistReconciliation.jsx
@@ -26,6 +26,7 @@ export default function ChecklistReconciliation(props) {
   // props.reviewer1Name - Display name for first reviewer
   // props.reviewer2Name - Display name for second reviewer
   // props.setNavbarStore - Store setter for navbar state (deep reactivity)
+  // props.getReconciliationNote - Function to get Y.Text for final reconciliation note (questionKey => Y.Text)
 
   // Track if we've initialized from saved progress
   const [initialized, setInitialized] = createSignal(false);
@@ -113,6 +114,18 @@ export default function ChecklistReconciliation(props) {
     return checklist[questionKey];
   };
 
+  // Get reviewer note for a question
+  // For multi-part questions (q9, q11), notes are stored at the parent level
+  const getReviewerNote = (checklist, questionKey) => {
+    if (!checklist) return '';
+    // For multi-part questions, the note is at the parent level (q9 or q11)
+    const noteData = checklist[questionKey];
+    if (noteData?.note !== undefined) {
+      return typeof noteData.note === 'string' ? noteData.note : noteData.note?.toString?.() || '';
+    }
+    return '';
+  };
+
   // Initialize final answers from saved progress or auto-fill agreements
   createEffect(() => {
     if (!props.checklist1 || initialized()) return;
@@ -334,6 +347,9 @@ export default function ChecklistReconciliation(props) {
               reviewer2Name={props.reviewer2Name || props.checklist2?.reviewerName || 'Reviewer 2'}
               isAgreement={currentComparison()?.isAgreement ?? true}
               isMultiPart={isMultiPartQuestion(currentQuestionKey())}
+              reviewer1Note={getReviewerNote(props.checklist1, currentQuestionKey())}
+              reviewer2Note={getReviewerNote(props.checklist2, currentQuestionKey())}
+              finalNoteYText={props.getReconciliationNote?.(currentQuestionKey())}
             />
 
             {/* Navigation Buttons */}
diff --git a/packages/web/src/components/checklist-ui/compare/MultiPartQuestionPage.jsx b/packages/web/src/components/checklist-ui/compare/MultiPartQuestionPage.jsx
index 3487b807b..367ff80d5 100644
--- a/packages/web/src/components/checklist-ui/compare/MultiPartQuestionPage.jsx
+++ b/packages/web/src/components/checklist-ui/compare/MultiPartQuestionPage.jsx
@@ -2,6 +2,7 @@ import { createSignal, createEffect, createMemo, For, Show } from 'solid-js';
 import { AMSTAR_CHECKLIST } from '@/AMSTAR2/checklist-map.js';
 import { getDataKeysForQuestion, getFinalAnswer } from '@/AMSTAR2/checklist-compare.js';
 import AnswerPanel from './AnswerPanel.jsx';
+import NotesCompareSection from './NotesCompareSection.jsx';
 
 /**
  * MultiPartQuestionPage - Handles q9 and q11 which have a/b parts
@@ -316,6 +317,18 @@ export default function MultiPartQuestionPage(props) {
           </For>
         </div>
       </div>
+
+      {/* Notes Section - One note for the entire multi-part question */}
+      <div class='px-4 pb-4'>
+        <NotesCompareSection
+          reviewer1Note={props.reviewer1Note}
+          reviewer2Note={props.reviewer2Note}
+          finalNoteYText={props.finalNoteYText}
+          reviewer1Name={props.reviewer1Name}
+          reviewer2Name={props.reviewer2Name}
+          collapsed={true}
+        />
+      </div>
     </div>
   );
 }
diff --git a/packages/web/src/components/checklist-ui/compare/NotesCompareSection.jsx b/packages/web/src/components/checklist-ui/compare/NotesCompareSection.jsx
new file mode 100644
index 000000000..f6add838d
--- /dev/null
+++ b/packages/web/src/components/checklist-ui/compare/NotesCompareSection.jsx
@@ -0,0 +1,254 @@
+/**
+ * NotesCompareSection - Side-by-side note comparison for reconciliation view
+ *
+ * Shows reviewer 1 and reviewer 2 notes (read-only) and allows editing the final note.
+ * Supports copying reviewer notes to the final note for convenience.
+ */
+import { createSignal, createEffect, onCleanup, Show } from 'solid-js';
+import { BiRegularChevronRight } from 'solid-icons/bi';
+import { BsJournalText, BsClipboard2 } from 'solid-icons/bs';
+import { Collapsible } from '@corates/ui';
+
+const MAX_LENGTH = 2000;
+const MAX_HEIGHT = 200;
+
+/**
+ * @param {Object} props
+ * @param {string} props.reviewer1Note - Text content of reviewer 1's note
+ * @param {string} props.reviewer2Note - Text content of reviewer 2's note
+ * @param {Y.Text} props.finalNoteYText - Y.Text instance for the final/reconciled note
+ * @param {string} props.reviewer1Name - Display name for reviewer 1
+ * @param {string} props.reviewer2Name - Display name for reviewer 2
+ * @param {boolean} [props.collapsed] - Start collapsed (default: true)
+ */
+export default function NotesCompareSection(props) {
+  // eslint-disable-next-line solid/reactivity -- intentionally read once for initial state
+  const [expanded, setExpanded] = createSignal(!props.collapsed);
+  const [finalNoteText, setFinalNoteText] = createSignal('');
+  let textareaRef;
+
+  const hasReviewer1Note = () => (props.reviewer1Note || '').trim().length > 0;
+  const hasReviewer2Note = () => (props.reviewer2Note || '').trim().length > 0;
+  const hasAnyNote = () =>
+    hasReviewer1Note() || hasReviewer2Note() || finalNoteText().trim().length > 0;
+
+  // Initialize from Y.Text and set up observer
+  createEffect(() => {
+    const yText = props.finalNoteYText;
+    if (!yText) {
+      setFinalNoteText('');
+      return;
+    }
+
+    // Get initial value
+    setFinalNoteText(yText.toString());
+
+    // Observe changes from other users
+    const observer = () => {
+      setFinalNoteText(yText.toString());
+    };
+
+    yText.observe(observer);
+
+    onCleanup(() => {
+      yText.unobserve(observer);
+    });
+  });
+
+  // Auto-resize textarea
+  createEffect(() => {
+    // Read finalNoteText to track text changes
+    finalNoteText();
+    if (textareaRef && expanded()) {
+      textareaRef.style.height = 'auto';
+      textareaRef.style.height = `${Math.min(textareaRef.scrollHeight, MAX_HEIGHT)}px`;
+    }
+  });
+
+  // Handle input for final note
+  function handleFinalNoteInput(e) {
+    const newValue = e.target.value;
+
+    // Enforce max length
+    if (newValue.length > MAX_LENGTH) {
+      e.target.value = newValue.slice(0, MAX_LENGTH);
+      return;
+    }
+
+    // Resize
+    e.target.style.height = 'auto';
+    e.target.style.height = `${Math.min(e.target.scrollHeight, MAX_HEIGHT)}px`;
+
+    const yText = props.finalNoteYText;
+    if (!yText) return;
+
+    // Update Y.Text
+    yText.doc.transact(() => {
+      yText.delete(0, yText.length);
+      yText.insert(0, newValue);
+    });
+  }
+
+  // Copy reviewer note to final note
+  function copyToFinal(sourceNote) {
+    const yText = props.finalNoteYText;
+    if (!yText || !sourceNote) return;
+
+    const text = sourceNote.slice(0, MAX_LENGTH);
+    yText.doc.transact(() => {
+      yText.delete(0, yText.length);
+      yText.insert(0, text);
+    });
+  }
+
+  // Merge both notes into final
+  function mergeToFinal() {
+    const yText = props.finalNoteYText;
+    if (!yText) return;
+
+    const parts = [];
+    if (hasReviewer1Note()) {
+      parts.push(`[${props.reviewer1Name || 'Reviewer 1'}]\n${props.reviewer1Note}`);
+    }
+    if (hasReviewer2Note()) {
+      parts.push(`[${props.reviewer2Name || 'Reviewer 2'}]\n${props.reviewer2Note}`);
+    }
+
+    const merged = parts.join('\n\n').slice(0, MAX_LENGTH);
+    yText.doc.transact(() => {
+      yText.delete(0, yText.length);
+      yText.insert(0, merged);
+    });
+  }
+
+  return (
+    <div class='mt-4 border-t border-gray-200 pt-3'>
+      <Collapsible
+        open={expanded()}
+        onOpenChange={setExpanded}
+        trigger={api => (
+          <div
+            {...api.getTriggerProps()}
+            class={`
+              flex items-center gap-1.5 py-1 text-sm cursor-pointer select-none
+              ${hasAnyNote() ? 'text-blue-600 hover:text-blue-700' : 'text-gray-500 hover:text-gray-700'}
+            `}
+          >
+            <BiRegularChevronRight
+              class={`w-4 h-4 shrink-0 transition-transform duration-200 ${expanded() ? 'rotate-90' : ''}`}
+            />
+            <BsJournalText class='w-4 h-4 shrink-0' />
+            <span class='font-medium'>Question Notes</span>
+            <Show when={hasAnyNote()}>
+              <span class='text-xs text-gray-400 ml-1'>
+                (
+                {[
+                  hasReviewer1Note() && 'R1',
+                  hasReviewer2Note() && 'R2',
+                  finalNoteText().trim() && 'Final',
+                ]
+                  .filter(Boolean)
+                  .join(', ')}
+                )
+              </span>
+            </Show>
+          </div>
+        )}
+      >
+        <div class='pt-3'>
+          {/* Three column layout for notes */}
+          <div class='grid grid-cols-3 gap-4'>
+            {/* Reviewer 1 Note (read-only) */}
+            <div class='bg-gray-50 rounded-lg p-3'>
+              <div class='flex items-center justify-between mb-2'>
+                <h4 class='text-xs font-semibold text-gray-700'>
+                  {props.reviewer1Name || 'Reviewer 1'}
+                </h4>
+                <Show when={hasReviewer1Note()}>
+                  <button
+                    onClick={() => copyToFinal(props.reviewer1Note)}
+                    class='text-xs text-blue-600 hover:text-blue-800 flex items-center gap-1'
+                    title='Copy to final note'
+                  >
+                    <BsClipboard2 class='w-3 h-3' />
+                    Use
+                  </button>
+                </Show>
+              </div>
+              <Show
+                when={hasReviewer1Note()}
+                fallback={<p class='text-xs text-gray-400 italic'>No note added</p>}
+              >
+                <p class='text-sm text-gray-700 whitespace-pre-wrap wrap-break-words'>
+                  {props.reviewer1Note}
+                </p>
+              </Show>
+            </div>
+
+            {/* Reviewer 2 Note (read-only) */}
+            <div class='bg-gray-50 rounded-lg p-3'>
+              <div class='flex items-center justify-between mb-2'>
+                <h4 class='text-xs font-semibold text-gray-700'>
+                  {props.reviewer2Name || 'Reviewer 2'}
+                </h4>
+                <Show when={hasReviewer2Note()}>
+                  <button
+                    onClick={() => copyToFinal(props.reviewer2Note)}
+                    class='text-xs text-blue-600 hover:text-blue-800 flex items-center gap-1'
+                    title='Copy to final note'
+                  >
+                    <BsClipboard2 class='w-3 h-3' />
+                    Use
+                  </button>
+                </Show>
+              </div>
+              <Show
+                when={hasReviewer2Note()}
+                fallback={<p class='text-xs text-gray-400 italic'>No note added</p>}
+              >
+                <p class='text-sm text-gray-700 whitespace-pre-wrap wrap-break-words'>
+                  {props.reviewer2Note}
+                </p>
+              </Show>
+            </div>
+
+            {/* Final Note (editable) */}
+            <div class='bg-green-50/50 rounded-lg p-3'>
+              <div class='flex items-center justify-between mb-2'>
+                <h4 class='text-xs font-semibold text-gray-700'>Final Note</h4>
+                <Show when={hasReviewer1Note() && hasReviewer2Note()}>
+                  <button
+                    onClick={mergeToFinal}
+                    class='text-xs text-green-600 hover:text-green-800'
+                    title='Merge both notes'
+                  >
+                    Merge Both
+                  </button>
+                </Show>
+              </div>
+              <Show
+                when={props.finalNoteYText}
+                fallback={<p class='text-xs text-gray-400 italic'>Loading...</p>}
+              >
+                <textarea
+                  ref={textareaRef}
+                  value={finalNoteText()}
+                  onInput={handleFinalNoteInput}
+                  placeholder='Add the final reconciled note...'
+                  class='w-full px-3 py-2 text-sm border rounded-lg resize-none overflow-hidden bg-white text-gray-900 focus:outline-none focus:ring-2 focus:ring-green-500 focus:border-transparent'
+                  style={{ 'min-height': '60px' }}
+                  maxLength={MAX_LENGTH}
+                />
+                <div class='flex justify-end mt-1 text-2xs text-gray-400'>
+                  <span class={finalNoteText().length > MAX_LENGTH * 0.9 ? 'text-amber-500' : ''}>
+                    {finalNoteText().length} / {MAX_LENGTH}
+                  </span>
+                </div>
+              </Show>
+            </div>
+          </div>
+        </div>
+      </Collapsible>
+    </div>
+  );
+}
diff --git a/packages/web/src/components/checklist-ui/compare/ReconciliationQuestionPage.jsx b/packages/web/src/components/checklist-ui/compare/ReconciliationQuestionPage.jsx
index fbce5a280..7b4e3eda3 100644
--- a/packages/web/src/components/checklist-ui/compare/ReconciliationQuestionPage.jsx
+++ b/packages/web/src/components/checklist-ui/compare/ReconciliationQuestionPage.jsx
@@ -3,6 +3,7 @@
  * Shows Reviewer 1, Reviewer 2, and Final (editable) answer panels side by side
  */
 import AnswerPanel from './AnswerPanel.jsx';
+import NotesCompareSection from './NotesCompareSection.jsx';
 import { createSignal, createEffect, Show } from 'solid-js';
 import { AMSTAR_CHECKLIST } from '@/AMSTAR2/checklist-map.js';
 import MultiPartQuestionPage from './MultiPartQuestionPage.jsx';
@@ -31,6 +32,9 @@ export default function ReconciliationQuestionPage(props) {
   // props.reviewer2Name
   // props.isAgreement - whether reviewers agree on this question
   // props.isMultiPart - whether this is a multi-part question (q9 or q11)
+  // props.reviewer1Note - text content of reviewer 1's note for this question
+  // props.reviewer2Note - text content of reviewer 2's note for this question
+  // props.finalNoteYText - Y.Text reference for the final reconciled note
 
   // For multi-part questions, delegate to MultiPartQuestionPage
   // Use Show for proper SolidJS reactivity
@@ -209,6 +213,18 @@ function SingleQuestionPage(props) {
           selectedSource={selectedSource()}
         />
       </div>
+
+      {/* Notes Section */}
+      <div class='px-4 pb-4'>
+        <NotesCompareSection
+          reviewer1Note={props.reviewer1Note}
+          reviewer2Note={props.reviewer2Note}
+          finalNoteYText={props.finalNoteYText}
+          reviewer1Name={props.reviewer1Name}
+          reviewer2Name={props.reviewer2Name}
+          collapsed={true}
+        />
+      </div>
     </div>
   );
 }
diff --git a/packages/web/src/components/checklist-ui/compare/ReconciliationWithPdf.jsx b/packages/web/src/components/checklist-ui/compare/ReconciliationWithPdf.jsx
index 13860624b..17a8d5eaa 100644
--- a/packages/web/src/components/checklist-ui/compare/ReconciliationWithPdf.jsx
+++ b/packages/web/src/components/checklist-ui/compare/ReconciliationWithPdf.jsx
@@ -26,6 +26,7 @@ export default function ReconciliationWithPdf(props) {
   // props.pdfs - Array of PDFs for multi-PDF selection
   // props.selectedPdfId - Currently selected PDF ID
   // props.onPdfSelect - Handler for PDF selection change
+  // props.getReconciliationNote - Function to get Y.Text for a reconciliation note (questionKey => Y.Text)
 
   // Layout state
   const [showPdf, setShowPdf] = createSignal(true);
@@ -165,6 +166,7 @@ export default function ReconciliationWithPdf(props) {
             onSaveReconciled={props.onSaveReconciled}
             onCancel={props.onCancel}
             setNavbarStore={setNavbarStore}
+            getReconciliationNote={props.getReconciliationNote}
           />
         </div>
 
diff --git a/packages/web/src/components/checklist-ui/compare/ReconciliationWrapper.jsx b/packages/web/src/components/checklist-ui/compare/ReconciliationWrapper.jsx
index 41b49637d..fa5ff88ad 100644
--- a/packages/web/src/components/checklist-ui/compare/ReconciliationWrapper.jsx
+++ b/packages/web/src/components/checklist-ui/compare/ReconciliationWrapper.jsx
@@ -26,6 +26,7 @@ export default function ReconciliationWrapper() {
     updateChecklist,
     getChecklistData,
     getReconciliationProgress,
+    getReconciliationNote,
     saveReconciliationProgress,
     clearReconciliationProgress,
     connect,
@@ -312,6 +313,7 @@ export default function ReconciliationWrapper() {
           pdfs={studyPdfs()}
           selectedPdfId={selectedPdfId()}
           onPdfSelect={handlePdfSelect}
+          getReconciliationNote={questionKey => getReconciliationNote(params.studyId, questionKey)}
         />
       </Show>
     </Show>
diff --git a/packages/web/src/primitives/useProject/checklists.js b/packages/web/src/primitives/useProject/checklists.js
index 8b825b8b6..23cb6d864 100644
--- a/packages/web/src/primitives/useProject/checklists.js
+++ b/packages/web/src/primitives/useProject/checklists.js
@@ -92,13 +92,35 @@ export function createChecklistOperations(projectId, getYDoc, isSynced) {
     const answersYMap = new Y.Map();
 
     if (type === CHECKLIST_TYPES.AMSTAR2) {
-      // AMSTAR2: Store each question as a nested Y.Map with answers and critical
+      // AMSTAR2: Store each question as a nested Y.Map with answers, critical, and note
+      // Note: q9 and q11 are multi-part questions (q9a/q9b, q11a/q11b) but get one note each
+      // at the parent level (q9, q11)
+      const multiPartParents = ['q9', 'q11'];
+      const subQuestionPattern = /^(q9|q11)[a-z]$/;
+
       Object.entries(answersData).forEach(([questionKey, questionData]) => {
         const questionYMap = new Y.Map();
         questionYMap.set('answers', questionData.answers);
         questionYMap.set('critical', questionData.critical);
+
+        // Add note for non-sub-questions
+        // Sub-questions (q9a, q9b, q11a, q11b) don't get notes - the parent does
+        if (!subQuestionPattern.test(questionKey)) {
+          questionYMap.set('note', new Y.Text());
+        }
+
         answersYMap.set(questionKey, questionYMap);
       });
+
+      // Add note entries for multi-part parent questions (q9, q11)
+      // These don't have answer data but need a note
+      multiPartParents.forEach(parentKey => {
+        if (!answersYMap.has(parentKey)) {
+          const parentYMap = new Y.Map();
+          parentYMap.set('note', new Y.Text());
+          answersYMap.set(parentKey, parentYMap);
+        }
+      });
     } else if (type === CHECKLIST_TYPES.ROBINS_I) {
       // ROBINS-I: Store each section/domain as nested Y.Maps to support concurrent edits
       Object.entries(answersData).forEach(([key, value]) => {
@@ -364,12 +386,20 @@ export function createChecklistOperations(projectId, getYDoc, isSynced) {
 
     const checklistType = checklistYMap.get('type');
 
-    // AMSTAR2: Store as nested Y.Map with answers and critical
+    // AMSTAR2: Store as nested Y.Map with answers and critical (preserving existing note)
     if (checklistType === 'AMSTAR2' && data.answers !== undefined) {
-      const questionYMap = new Y.Map();
+      let questionYMap = answersMap.get(key);
+      if (!questionYMap || !(questionYMap instanceof Y.Map)) {
+        questionYMap = new Y.Map();
+        answersMap.set(key, questionYMap);
+      }
       questionYMap.set('answers', data.answers);
       questionYMap.set('critical', data.critical);
-      answersMap.set(key, questionYMap);
+      // Note: Y.Text note is preserved - we don't overwrite it here
+      // If no note exists yet, create one (for existing checklists without notes)
+      if (!questionYMap.get('note')) {
+        questionYMap.set('note', new Y.Text());
+      }
     }
     // ROBINS-I: Update nested Y.Maps granularly for concurrent edit support
     else if (checklistType === 'ROBINS_I') {
@@ -453,6 +483,49 @@ export function createChecklistOperations(projectId, getYDoc, isSynced) {
     checklistYMap.set('updatedAt', Date.now());
   }
 
+  /**
+   * Get a Y.Text reference for a question's note (for direct binding)
+   * @param {string} studyId - The study ID
+   * @param {string} checklistId - The checklist ID
+   * @param {string} questionKey - The question key (e.g., 'q1', 'q9' for multi-part)
+   * @returns {Y.Text|null} The Y.Text reference or null
+   */
+  function getQuestionNote(studyId, checklistId, questionKey) {
+    const ydoc = getYDoc();
+    if (!ydoc) return null;
+
+    const studiesMap = ydoc.getMap('reviews');
+    const studyYMap = studiesMap.get(studyId);
+    if (!studyYMap) return null;
+
+    const checklistsMap = studyYMap.get('checklists');
+    if (!checklistsMap) return null;
+
+    const checklistYMap = checklistsMap.get(checklistId);
+    if (!checklistYMap) return null;
+
+    const answersMap = checklistYMap.get('answers');
+    if (!answersMap) return null;
+
+    const questionYMap = answersMap.get(questionKey);
+    if (!questionYMap || !(questionYMap instanceof Y.Map)) return null;
+
+    const note = questionYMap.get('note');
+    // Return existing note, or create one if missing (for existing checklists)
+    if (note instanceof Y.Text) {
+      return note;
+    }
+
+    // Create note if it doesn't exist (backward compatibility)
+    if (isSynced()) {
+      const newNote = new Y.Text();
+      questionYMap.set('note', newNote);
+      return newNote;
+    }
+
+    return null;
+  }
+
   return {
     createChecklist,
     updateChecklist,
@@ -460,5 +533,6 @@ export function createChecklistOperations(projectId, getYDoc, isSynced) {
     getChecklistAnswersMap,
     getChecklistData,
     updateChecklistAnswer,
+    getQuestionNote,
   };
 }
diff --git a/packages/web/src/primitives/useProject/index.js b/packages/web/src/primitives/useProject/index.js
index 975f7b485..55aa090d5 100644
--- a/packages/web/src/primitives/useProject/index.js
+++ b/packages/web/src/primitives/useProject/index.js
@@ -184,6 +184,7 @@ export function useProject(projectId) {
     getChecklistAnswersMap: (...args) => checklistOps?.getChecklistAnswersMap(...args),
     getChecklistData: (...args) => checklistOps?.getChecklistData(...args),
     updateChecklistAnswer: (...args) => checklistOps?.updateChecklistAnswer(...args),
+    getQuestionNote: (...args) => checklistOps?.getQuestionNote(...args),
 
     // PDF operations
     addPdfToStudy: (...args) => pdfOps?.addPdfToStudy(...args),
@@ -197,6 +198,7 @@ export function useProject(projectId) {
     // Reconciliation operations
     saveReconciliationProgress: (...args) => reconciliationOps?.saveReconciliationProgress(...args),
     getReconciliationProgress: (...args) => reconciliationOps?.getReconciliationProgress(...args),
+    getReconciliationNote: (...args) => reconciliationOps?.getReconciliationNote(...args),
     clearReconciliationProgress: (...args) =>
       reconciliationOps?.clearReconciliationProgress(...args),
 
diff --git a/packages/web/src/primitives/useProject/reconciliation.js b/packages/web/src/primitives/useProject/reconciliation.js
index 92008c140..ce504670f 100644
--- a/packages/web/src/primitives/useProject/reconciliation.js
+++ b/packages/web/src/primitives/useProject/reconciliation.js
@@ -1,5 +1,8 @@
 /**
  * Reconciliation progress operations for useProject
+ *
+ * Note: finalAnswers are stored as a nested Y.Map structure to enable
+ * collaborative editing of notes during reconciliation.
  */
 
 import * as Y from 'yjs';
@@ -14,6 +17,7 @@ import * as Y from 'yjs';
 export function createReconciliationOperations(projectId, getYDoc, isSynced) {
   /**
    * Save reconciliation progress for a study
+   * Uses Y.Map for finalAnswers to enable collaborative note editing
    * @param {string} studyId - The study ID
    * @param {Object} progressData - Progress data { checklist1Id, checklist2Id, currentPage, viewMode, finalAnswers }
    */
@@ -37,9 +41,38 @@ export function createReconciliationOperations(projectId, getYDoc, isSynced) {
     reconciliationMap.set('checklist2Id', progressData.checklist2Id);
     reconciliationMap.set('currentPage', progressData.currentPage);
     reconciliationMap.set('viewMode', progressData.viewMode || 'questions');
-    reconciliationMap.set('finalAnswers', JSON.stringify(progressData.finalAnswers || {}));
     reconciliationMap.set('updatedAt', Date.now());
 
+    // Store finalAnswers as a nested Y.Map for collaborative editing
+    let finalAnswersMap = reconciliationMap.get('finalAnswers');
+    if (!finalAnswersMap || !(finalAnswersMap instanceof Y.Map)) {
+      finalAnswersMap = new Y.Map();
+      reconciliationMap.set('finalAnswers', finalAnswersMap);
+    }
+
+    // Update each question's answers
+    const finalAnswers = progressData.finalAnswers || {};
+    Object.entries(finalAnswers).forEach(([questionKey, questionData]) => {
+      let questionYMap = finalAnswersMap.get(questionKey);
+      if (!questionYMap || !(questionYMap instanceof Y.Map)) {
+        questionYMap = new Y.Map();
+        finalAnswersMap.set(questionKey, questionYMap);
+      }
+
+      // Store answers and critical flag
+      if (questionData.answers !== undefined) {
+        questionYMap.set('answers', questionData.answers);
+      }
+      if (questionData.critical !== undefined) {
+        questionYMap.set('critical', questionData.critical);
+      }
+
+      // Initialize Y.Text for note if not present (for collaborative editing)
+      if (!questionYMap.get('note')) {
+        questionYMap.set('note', new Y.Text());
+      }
+    });
+
     studyYMap.set('updatedAt', Date.now());
   }
 
@@ -59,19 +92,92 @@ export function createReconciliationOperations(projectId, getYDoc, isSynced) {
     const reconciliationMap = studyYMap.get('reconciliation');
     if (!reconciliationMap) return null;
 
-    const data = reconciliationMap.toJSON ? reconciliationMap.toJSON() : {};
-    if (!data.checklist1Id || !data.checklist2Id) return null;
+    const checklist1Id = reconciliationMap.get('checklist1Id');
+    const checklist2Id = reconciliationMap.get('checklist2Id');
+    if (!checklist1Id || !checklist2Id) return null;
+
+    // Extract finalAnswers from Y.Map structure
+    const finalAnswers = {};
+    const finalAnswersMap = reconciliationMap.get('finalAnswers');
+    if (finalAnswersMap && finalAnswersMap instanceof Y.Map) {
+      for (const [questionKey, questionYMap] of finalAnswersMap.entries()) {
+        if (questionYMap instanceof Y.Map) {
+          finalAnswers[questionKey] = {
+            answers: questionYMap.get('answers'),
+            critical: questionYMap.get('critical'),
+            // Note: Y.Text note is accessed separately via getReconciliationNote
+          };
+        }
+      }
+    }
 
     return {
-      checklist1Id: data.checklist1Id,
-      checklist2Id: data.checklist2Id,
-      currentPage: data.currentPage || 0,
-      viewMode: data.viewMode || 'questions',
-      finalAnswers: data.finalAnswers ? JSON.parse(data.finalAnswers) : {},
-      updatedAt: data.updatedAt,
+      checklist1Id,
+      checklist2Id,
+      currentPage: reconciliationMap.get('currentPage') || 0,
+      viewMode: reconciliationMap.get('viewMode') || 'questions',
+      finalAnswers,
+      updatedAt: reconciliationMap.get('updatedAt'),
     };
   }
 
+  /**
+   * Get a Y.Text reference for a reconciliation note (for direct binding)
+   * @param {string} studyId - The study ID
+   * @param {string} questionKey - The question key (e.g., 'q1', 'q9')
+   * @returns {Y.Text|null} The Y.Text reference or null
+   */
+  function getReconciliationNote(studyId, questionKey) {
+    const ydoc = getYDoc();
+    if (!ydoc) return null;
+
+    const studiesMap = ydoc.getMap('reviews');
+    const studyYMap = studiesMap.get(studyId);
+    if (!studyYMap) return null;
+
+    // Create reconciliation map if it doesn't exist
+    let reconciliationMap = studyYMap.get('reconciliation');
+    if (!reconciliationMap) {
+      if (!isSynced()) return null;
+      reconciliationMap = new Y.Map();
+      studyYMap.set('reconciliation', reconciliationMap);
+    }
+
+    // Create finalAnswers map if it doesn't exist
+    let finalAnswersMap = reconciliationMap.get('finalAnswers');
+    if (!finalAnswersMap || !(finalAnswersMap instanceof Y.Map)) {
+      if (!isSynced()) return null;
+      finalAnswersMap = new Y.Map();
+      reconciliationMap.set('finalAnswers', finalAnswersMap);
+    }
+
+    let questionYMap = finalAnswersMap.get(questionKey);
+    if (!questionYMap || !(questionYMap instanceof Y.Map)) {
+      // Create the question map if it doesn't exist
+      if (isSynced()) {
+        questionYMap = new Y.Map();
+        questionYMap.set('note', new Y.Text());
+        finalAnswersMap.set(questionKey, questionYMap);
+        return questionYMap.get('note');
+      }
+      return null;
+    }
+
+    let note = questionYMap.get('note');
+    if (note instanceof Y.Text) {
+      return note;
+    }
+
+    // Create note if missing
+    if (isSynced()) {
+      note = new Y.Text();
+      questionYMap.set('note', note);
+      return note;
+    }
+
+    return null;
+  }
+
   /**
    * Clear reconciliation progress for a study
    * @param {string} studyId - The study ID
@@ -91,6 +197,7 @@ export function createReconciliationOperations(projectId, getYDoc, isSynced) {
   return {
     saveReconciliationProgress,
     getReconciliationProgress,
+    getReconciliationNote,
     clearReconciliationProgress,
   };
 }
diff --git a/packages/web/src/primitives/useProjectPdfHandlers.js b/packages/web/src/primitives/useProjectPdfHandlers.js
index 4c5242bab..fa355d0c3 100644
--- a/packages/web/src/primitives/useProjectPdfHandlers.js
+++ b/packages/web/src/primitives/useProjectPdfHandlers.js
@@ -8,7 +8,7 @@
  * - secondary: Additional supplementary PDFs (default)
  */
 
-import { uploadPdf, deletePdf, downloadPdf, getPdfUrl } from '@api/pdf-api.js';
+import { uploadPdf, deletePdf, downloadPdf } from '@api/pdf-api.js';
 import { cachePdf, removeCachedPdf, getCachedPdf } from '@primitives/pdfCache.js';
 import projectStore from '@/stores/projectStore.js';
 import pdfPreviewStore from '@/stores/pdfPreviewStore.js';