Thanks for the reply - I've deleted the file, logged in and resynced play counts, but it still seems to be pulling old ones. Is there anywhere else it could be pulling the counts from?
Edit: I've found LastFmScrobble.txt in the roaming file, which has stored all of these plays, and I suspect is where Musicbee might be pulling from. Even after deleting it though, it still seems to find them somewhere!