There are a few ways to accomplish, but they all revolve around working with sets of tracks that can be matched up.
If you store the rating in the MusicBee database rather than inside a tag, and then replace the files in explorer with files with an identical filename, then inside MusicBee simply rescan these files, MusicBee will refresh the data that isn't stored in the database, with fresh info from the new file tags - rating will be retained.
If the filename isn't identical - MusicBee will create a new database entry for the new track.