It's been a while since I've done this but it should still work. Select all files, tools, tagging tools, reset play count. After it finishes close MusicBee, in Windows Explorer go to c:(or whatever drive letter)\users\(username)\appdata\roaming\musicbee\internalcache and rename lastfmplaycountcache.dat from .dat to .old. When you open MusicBee again it should update the files using the correct last.fm account.
If it's successful you can go back and delete the .old file.
This is assuming it's a full install, if it's a portable one, the file should be in the installation folder under AppData\InternalCache.