I'm still hoping we don't have to go the route of losing a bunch of info, as you say. Also, we can definitely give you some tips on how to make sure things are saved in the file, to protect against future instances of this.
But as a next step in troubleshooting, try browsing to one of the files using MusicBee's Computer node. Then right click and select "Send to" (but don't click on anything else, you're just looking). Is Inbox or Music Library grayed out? (Hopefully it's not Audiobooks!)
(And yeah, MusicBee does all duplicate comparisons based on metadata. You can use it to convert file paths to tags, too, though.)