This keeps happening to me all the time. I create a playlist and it will work just fine for days, weeks, sometimes months. But then, randomly one day, all the playlist will become empty. The tracks are still in the server, but the playlists created from these tracks are empty.
The only a few factors that I can figure would be relevant in this case. My Plex server is a linux VM attached to a NSA via a network connection. I have an insane number of songs, about 80k.
could be as simple as Plex temporarily losing access to your files during an automated/periodic library scan (e.g. if the network drive was asleep and takes too long to spin up). If your server is configured to automatically empty its trash after every scan, this can result in the items being dropped from your library (incl. their playlist assignments). If the drive is ready during a subsequent scan, the files will be re-added (though without your previous manual edits and playlist assignments).
If this can happen in your setup, make sure to disable Settings > [Server Name] > Library > Empty trash automatically after every scan
