diff --git a/src/crates/core/src/agentic/coordination/coordinator.rs b/src/crates/core/src/agentic/coordination/coordinator.rs
index d23abf1f..758d8efb 100644
--- a/src/crates/core/src/agentic/coordination/coordinator.rs
+++ b/src/crates/core/src/agentic/coordination/coordinator.rs
@@ -17,7 +17,9 @@ use crate::agentic::image_analysis::ImageContextData;
 use crate::agentic::session::SessionManager;
 use crate::agentic::tools::pipeline::{SubagentParentInfo, ToolPipeline};
 use crate::agentic::WorkspaceBinding;
-use crate::service::bootstrap::is_workspace_bootstrap_pending;
+use crate::service::bootstrap::{
+    initialize_workspace_persona_files, is_workspace_bootstrap_pending,
+};
 use crate::util::errors::{BitFunError, BitFunResult};
 use log::{debug, error, info, warn};
 use std::path::{Path, PathBuf};
@@ -633,7 +635,11 @@ Update the persona files and delete BOOTSTRAP.md as soon as bootstrap is complet
         workspace_path: String,
     ) -> BitFunResult<AssistantBootstrapEnsureOutcome> {
         let workspace_root = PathBuf::from(&workspace_path);
-        if !is_workspace_bootstrap_pending(&workspace_root) {
+        // Empty or partial assistant dirs may never have run create_assistant_workspace; fill only
+        // missing persona stubs (never overwrite). Ensures BOOTSTRAP.md exists when appropriate.
+        initialize_workspace_persona_files(&workspace_root).await?;
+        let bootstrap_pending = is_workspace_bootstrap_pending(&workspace_root);
+        if !bootstrap_pending {
             return Ok(AssistantBootstrapEnsureOutcome::Skipped {
                 session_id,
                 reason: AssistantBootstrapSkipReason::BootstrapNotRequired,
@@ -649,7 +655,9 @@ Update the persona files and delete BOOTSTRAP.md as soon as bootstrap is complet
             }
         };
 
-        if self.session_manager.get_turn_count(&session_id) > 0 {
+        let turn_count = self.session_manager.get_turn_count(&session_id);
+
+        if turn_count > 0 {
             return Ok(AssistantBootstrapEnsureOutcome::Skipped {
                 session_id,
                 reason: AssistantBootstrapSkipReason::SessionHasExistingTurns,
diff --git a/src/crates/core/src/service/workspace/service.rs b/src/crates/core/src/service/workspace/service.rs
index 6ce0c5cc..3e1be696 100644
--- a/src/crates/core/src/service/workspace/service.rs
+++ b/src/crates/core/src/service/workspace/service.rs
@@ -242,6 +242,7 @@ impl WorkspaceService {
             })?;
         }
 
+        // New assistant dirs get persona files at creation; coordinator also fills missing files when opening.
         initialize_workspace_persona_files(&path).await?;
 
         self.create_workspace(path, options).await
diff --git a/src/web-ui/src/app/components/NavPanel/sections/workspaces/WorkspaceItem.tsx b/src/web-ui/src/app/components/NavPanel/sections/workspaces/WorkspaceItem.tsx
index 1b005116..45580ce3 100644
--- a/src/web-ui/src/app/components/NavPanel/sections/workspaces/WorkspaceItem.tsx
+++ b/src/web-ui/src/app/components/NavPanel/sections/workspaces/WorkspaceItem.tsx
@@ -199,6 +199,8 @@ const WorkspaceItem: React.FC<WorkspaceItemProps> = ({
       await flowChatManager.resetWorkspaceSessions(workspace.rootPath, {
         reinitialize: isActive,
         preferredMode: 'Claw',
+        ensureAssistantBootstrap:
+          isActive && workspace.workspaceKind === WorkspaceKind.Assistant,
       });
       notificationService.success(t('nav.workspaces.workspaceReset'), { duration: 2500 });
     } catch (error) {
diff --git a/src/web-ui/src/flow_chat/services/FlowChatManager.ts b/src/web-ui/src/flow_chat/services/FlowChatManager.ts
index 265d2ba3..a7d44d65 100644
--- a/src/web-ui/src/flow_chat/services/FlowChatManager.ts
+++ b/src/web-ui/src/flow_chat/services/FlowChatManager.ts
@@ -153,7 +153,12 @@ export class FlowChatManager {
 
   async resetWorkspaceSessions(
     workspacePath: string,
-    options?: { reinitialize?: boolean; preferredMode?: string }
+    options?: {
+      reinitialize?: boolean;
+      preferredMode?: string;
+      /** After reinit, ask core to run assistant bootstrap if BOOTSTRAP.md is present (e.g. workspace reset). */
+      ensureAssistantBootstrap?: boolean;
+    }
   ): Promise<void> {
     const removedSessionIds = this.context.flowChatStore.removeSessionsByWorkspace(workspacePath);
 
@@ -180,6 +185,24 @@ export class FlowChatManager {
     if (!hasHistoricalSessions || !hasActiveWorkspaceSession) {
       await this.createChatSession({}, options.preferredMode);
     }
+
+    if (options?.ensureAssistantBootstrap) {
+      const sid = this.context.flowChatStore.getState().activeSessionId;
+      if (sid) {
+        try {
+          const { agentAPI } = await import('@/infrastructure/api/service-api/AgentAPI');
+          await agentAPI.ensureAssistantBootstrap({
+            sessionId: sid,
+            workspacePath,
+          });
+        } catch (error) {
+          log.warn('ensureAssistantBootstrap after resetWorkspaceSessions failed', {
+            workspacePath,
+            error,
+          });
+        }
+      }
+    }
   }
 
   async sendMessage(