I’ve had a folder where I put my newest TV shows and it was working fine. After I finished watching the show, I’d get it out of that folder. I recently changed something and I’m not sure what. Now when I move them out of that folder or delete them their ghosts stay behind in plex.
It appears you have disabled Settings > [Server Name] > Library > Empty trash automatically after every scan. In this configuration you need to manually empty your library’s trash.
Personally I’m a fan of disabling the automatic emptying of trash. This helps to avoid losing custom edits if a drive is temporarily not available or too slow to spin up during an automatic/scheduled scan.