Not necessarily. As long as your meta tags are consistent, it might work with music.
Avoid using the pre-defined structure for your data. It works much better with a separated folder location.
Make a backup copy of your Plex database prior to editing it. That way you can restore it if you mess up. [HowTo] Plex database modification - Moving media the right/wrong way - #10 by jelwell
But this will only fix the database.
The cover art selections are stored in hard links, (i.e directly in the file system and not in the database) which have already been destroyed by your backup process.