Part of the problem is Plex is scanning the #snapshot folders. This will be fixed in an upcoming release (date tbd).
In the meantime, make the #snapshot folder invisible to Plex.
See: Scan results in hundreds of duplicate items in Music Library - #18 by Kubjo
Once that is done:
- Re-scan all libraries
- Empty Trash
- Clean Bundles
After the scan/empty trash/clean bundles is complete:
- Stop Plex Media Server and wait one minute.
- Start Plex Media Server and wait three minutes for Plex to log the startup sequence.
- Pull the server log files (Settings → Troubleshooting).
- Upload the entire zip file to the thread (drag it into the message window, it will insert at the cursor location).
We can then see if anything else needs addressing.