diff --git a/backend/app/usecases/bot.py b/backend/app/usecases/bot.py
index 1fa985259..3b17a4ebd 100644
--- a/backend/app/usecases/bot.py
+++ b/backend/app/usecases/bot.py
@@ -96,7 +96,10 @@ def _update_s3_documents_by_diff(
 
     for filename in deleted_filenames:
         document_path = compose_upload_document_s3_path(user_id, bot_id, filename)
-        delete_file_from_s3(DOCUMENT_BUCKET, document_path)
+
+        # Ignore errors when deleting a non-existent file from the S3 bucket used in knowledge bases.
+        # This allows users to update bot if the uploaded file is missing after the bot is created.
+        delete_file_from_s3(DOCUMENT_BUCKET, document_path, ignore_not_exist=True)
 
 
 def create_new_bot(user_id: str, bot_input: BotInput) -> BotOutput:
@@ -815,8 +818,12 @@ def issue_presigned_url(
 
 
 def remove_uploaded_file(user_id: str, bot_id: str, filename: str):
+    # Ignore errors when deleting a non-existent file from the S3 bucket used in knowledge bases.
+    # This allows users to update bot if the uploaded file is missing after the bot is created.
     delete_file_from_s3(
-        DOCUMENT_BUCKET, compose_upload_temp_s3_path(user_id, bot_id, filename)
+        DOCUMENT_BUCKET,
+        compose_upload_temp_s3_path(user_id, bot_id, filename),
+        ignore_not_exist=True,
     )
     return
 
diff --git a/backend/app/utils.py b/backend/app/utils.py
index 265985832..d777f6409 100644
--- a/backend/app/utils.py
+++ b/backend/app/utils.py
@@ -97,17 +97,18 @@ def compose_upload_document_s3_path(user_id: str, bot_id: str, filename: str) ->
     return f"{user_id}/{bot_id}/documents/{filename}"
 
 
-def delete_file_from_s3(bucket: str, key: str):
+def delete_file_from_s3(bucket: str, key: str, ignore_not_exist: bool = False):
     client = boto3.client("s3", region_name=BEDROCK_REGION)
 
     # Check if the file exists
-    try:
-        client.head_object(Bucket=bucket, Key=key)
-    except ClientError as e:
-        if e.response["Error"]["Code"] == "404":
-            raise FileNotFoundError(f"The file does not exist in bucket.")
-        else:
-            raise
+    if not ignore_not_exist:
+        try:
+            client.head_object(Bucket=bucket, Key=key)
+        except ClientError as e:
+            if e.response["Error"]["Code"] == "404":
+                raise FileNotFoundError(f"The file does not exist in bucket.")
+            else:
+                raise
 
     response = client.delete_object(Bucket=bucket, Key=key)
     return response