I assume because:
Your media storage is external to the Plex server device
and you have “Automatically empty trash” enabled.
Apparently there are times when your media storage is not responding (either not fast enough or not at all). This then makes Plex assuming that the media have been deleted. And the automatic trash cleaning is removing them from the library, thus removing all your customized metadata as well.
Then when you start a new library scan, all those files are found again and added “as new”.
Solution:
Never activate “Empty trash automatically” if your media storage is not inside the server machine. Make sure that Plex server always has access to your media storage, as long as it is running. Particularly if you have automatic and/or periodic library scans activated.
Settings - Server - Library
