I had to reload all the audio files (and uninstall and reinstall the Drupal Audio module), so all the music is back and Flash-playable. However, all the notes are (at least temporarily) gone. I also seem to have uncovered a nasty bug as well, where when one bit of Audio metadata is edited from within Drupal, all of it gets strangely truncated and has to be hand-edited in the MySQL tables (which I had to do FOR EVERY SONG). I'm not too happy with that state of affairs.
I'd say things are 90% back to normal. Still some more testing to do, and resolution for the issue I'm encountering and then we'll be at 100%. Unless of course, someone has a better idea?
Update: upgrading to the latest beta of the getID3 library seems to have fixed the truncation problem. We're all good now. Upload away!