Among the list of folders which are connected to your library, there is probably one which is either
- completely empty
- inaccessible
- invalid / not existent
This will cause the “Empty Trash” command to be ignored. It is a safety feature, which avoids you losing your library when media storage is temporarily unavailable.
Another possible reason can be a damaged database:
- activate debug logging (not ‘verbose’!)
- quit Plex Server
- wait 1 minute
- start Plex Server
- wait 5 minutes
- fetch log files and attach them here
Or inspect them yourself. Take a look at the Plex Media Server.log file and seek for messages about database corrupt or malformed.
If you find these, you may have to repair your database.
https://support.plex.tv/articles/repair-a-corrupted-database/
