Is there anyway to undo the corruption to the filesystem without losing music?

Once a new-scheme file exists, the player will use that from then on, until the FID is deleted and re-created -- even though all FIDs created by the player (e.g. when told to do so by Emplode/Jemplode/Emptool) will be old-scheme.

This means that, for FIDs that exist both as new-scheme and old-scheme, the new-scheme one is the one the player is using, and thus probably the one you want (but check a few first with "ls -l" to make sure you're keeping the newer one).

Peter