diff --git a/backend/open_webui/routers/knowledge.py b/backend/open_webui/routers/knowledge.py
index 6c7bdc64dc..020cf00144 100644
--- a/backend/open_webui/routers/knowledge.py
+++ b/backend/open_webui/routers/knowledge.py
@@ -1057,14 +1057,24 @@ async def remove_file_from_knowledge_by_id(
                 pass
 
             # Delete the object-storage blob before dropping the DB row so we
-            # still have file.path available; previously this endpoint only
-            # removed the DB record and orphaned the blob in S3/GCS/local.
+            # still have file.path available. If storage deletion fails we
+            # must NOT drop the DB row: a transient S3/GCS failure would
+            # otherwise leave an orphan blob with no metadata to retry
+            # against. Keeping the file row lets an operator re-issue the
+            # delete once the backend recovers.
             try:
                 Storage.delete_file(file.path)
             except Exception as storage_err:
-                log.warning(
+                log.exception(
                     f'Failed to delete storage blob for {form_data.file_id}: {storage_err}'
                 )
+                raise HTTPException(
+                    status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
+                    detail=(
+                        'File unlinked from knowledge base, but deleting the '
+                        'stored blob failed; file record kept for retry.'
+                    ),
+                )
 
             # Delete file from database
             await Files.delete_file_by_id(form_data.file_id, db=db)
diff --git a/src/lib/components/workspace/Knowledge/KnowledgeBase.svelte b/src/lib/components/workspace/Knowledge/KnowledgeBase.svelte
index f04d0efea1..8d9e7e968a 100644
--- a/src/lib/components/workspace/Knowledge/KnowledgeBase.svelte
+++ b/src/lib/components/workspace/Knowledge/KnowledgeBase.svelte
@@ -481,9 +481,15 @@
 	            // files, or we resolve with an empty list and the caller's
 	            // existing empty-check toasts.
 	            let settled = false;
+	            let changeStarted = false;
+	            let focusTimer: ReturnType<typeof setTimeout> | null = null;
 	            const finish = (err?: unknown) => {
 	                if (settled) return;
 	                settled = true;
+	                if (focusTimer !== null) {
+	                    clearTimeout(focusTimer);
+	                    focusTimer = null;
+	                }
 	                if (input.parentNode) {
 	                    input.parentNode.removeChild(input);
 	                }
@@ -496,11 +502,25 @@
 	            };
 	            const onFocus = () => {
 	                // 'change' fires after 'focus' returns to the window, so
-	                // wait briefly before deciding the user cancelled.
-	                setTimeout(() => finish(), 500);
+	                // wait briefly before deciding the user cancelled. If a
+	                // change event actually started handling files before the
+	                // timer expires, changeStarted gates finish() so we don't
+	                // resolve in the middle of hashing a large batch with a
+	                // partial files array.
+	                focusTimer = setTimeout(() => {
+	                    focusTimer = null;
+	                    if (!changeStarted) {
+	                        finish();
+	                    }
+	                }, 500);
 	            };
 
 	            input.onchange = async () => {
+	                changeStarted = true;
+	                if (focusTimer !== null) {
+	                    clearTimeout(focusTimer);
+	                    focusTimer = null;
+	                }
 	                try {
 	                    const inputFiles = Array.from(input.files || []).filter(
 	                        (file) => !hasHiddenFolder(file.webkitRelativePath) && !file.name.startsWith('.')