Thanks for the suggestion.
Turns out, that if I turn off "update media daemon", move the file out to a temp directory, resynchronize via web-admin, delete files not in database via web-admin, remove the coverart using mediamonkey, wipe all Id3v1 and Id3v2 tags using mediamonkey, resynchronize tags to mediamonkey's database, move the file back to the /audio directory, resynchronize via web-admin, it works.
(At least it did with one mp3. I'm going to try the above process for my whole library next).