diff --git a/server/mergin/sync/files.py b/server/mergin/sync/files.py
index f0ee09a1..d22358d5 100644
--- a/server/mergin/sync/files.py
+++ b/server/mergin/sync/files.py
@@ -286,8 +286,6 @@ def to_data_delta(self):
             change=self.change,
             version=self.version,
         )
-        if self.diffs:
-            result.diff = self.diffs[0].id
         return result
 
 
@@ -332,6 +330,9 @@ def make_object(self, data, **kwargs):
 
     @post_dump
     def patch_field(self, data, **kwargs):
+        assert data.get("change") != PushChangeType.UPDATE_DIFF.value or data.get(
+            "diff"
+        ), "Diff file must be provided for update_diff change type"
         # drop 'diff' key entirely if empty or None as database would expect
         if not data.get("diff"):
             data.pop("diff", None)
diff --git a/server/mergin/sync/models.py b/server/mergin/sync/models.py
index bc01c523..e5f5123d 100644
--- a/server/mergin/sync/models.py
+++ b/server/mergin/sync/models.py
@@ -1030,7 +1030,9 @@ def construct_checkpoint(self) -> bool:
             return False
 
         project: Project = basefile.file.project
-        os.makedirs(project.storage.diffs_dir, exist_ok=True)
+
+        # create diffs directory if not exists and subfolders in case of diffs/subfolder/diff-file
+        os.makedirs(os.path.dirname(self.abs_path), exist_ok=True)
 
         try:
             if len(diffs_paths) == 1:
@@ -1041,7 +1043,7 @@ def construct_checkpoint(self) -> bool:
                 project.storage.geodiff.concat_changes(diffs_paths, self.abs_path)
         except (GeoDiffLibError, GeoDiffLibConflictError):
             logging.error(
-                f"Geodiff: Failed to merge diffs for file {self.file_path_id}"
+                f"Geodiff: Failed to merge diffs for file {self.file_path_id}."
             )
             return False
 
@@ -1357,6 +1359,11 @@ def create_checkpoint(
                     # Patch the delta with the path to the new diff checkpoint
                     item.diff = checkpoint_diff.path
                     db.session.add(checkpoint_diff)
+                else:
+                    # checkpoint already exists, just patch the delta with the path to the existing diff checkpoint
+                    # this could happen when file diff exists but dela was missing
+                    # this allowing us to remove rank > 0 delta checkpoints in case of inconsistencies
+                    item.diff = existing_diff_checkpoint.path
 
         checkpoint_delta = ProjectVersionDelta(
             project_id=project_id,