GitHub user cookesan added a comment to the discussion: S3 Dag Bundle won't 
remove files removed on remote S3

The current source says stale local files should be deleted.

`S3DagBundle.refresh()` calls `S3Hook.sync_to_local_dir(..., 
delete_stale=True)`, and `sync_to_local_dir()` has a stale-file cleanup path 
that removes local files not present in the current S3 object list.

So I would first check the exact Airflow and `apache-airflow-providers-amazon` 
versions in the environment. If your installed provider version predates that 
`delete_stale=True` behavior, upgrading the Amazon provider may be the fix.

If you are already on a version with that code, then this is probably worth a 
small reproducible bug report: bucket prefix, bundle config, provider version, 
whether the deleted file is under the configured prefix, and debug logs from 
`S3Hook.sync_to_local_dir()`.

GitHub link: 
https://github.com/apache/airflow/discussions/64775#discussioncomment-16657270

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