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Out of interest, does the MB database need to sync with meta data on the files or is it a live call that should show any tags that are added in MP3Tag immediately?
Just addressing this part, if you add/change any tags on library files using an external tagger like Mp3tag instead via MusicBee's own tag editor, you must rescan the files in MusicBee for it to pick up the changes (right-click, SendTo->File Rescan, or for a whole library, Tools->Advanced->Rescan All Files).
I would expect them all to not work if that was the issue.
I would but it's a big job to remove 20,000 comment tags and then be sure I can restore them successfully.