If I may augment here?
Is this for every file or a selected few?
If a selected few, “Plex Dance” that media.
(move out, scan files, empty trash, clean bundles, optimize DB, move back)
I’ve seen this happen a few times but don’t yet have enough information to start reproducing / tracking it down.
I suspect it has something to do with hard shutdown/restart of PMS (possibly crash & restart) which causes DB pointers to be criss-crossed in the records.