I’m not aware of any general issue with movie libraries.
Your server logs should show if there’s maybe some issue with your database – if so, you could attempt to repair the database.
Given you mention the server used to add some of the files to your library earlier, this is probably not related to some weird unsupported file formats or bad file naming.
https://support.plex.tv/articles/201543057-why-is-some-of-my-content-not-found/
