% cd ~/Library/Mail/IMAP:account@hostname/ % rm -rf Deleted Messages.imapmbox INBOX.imapmbox Junk.imapmboxAt that point, I got back into mail.app, it re-synced and everything looked normal. The only thing that I can figure out is that some signature matched between old, deleted email and new email. Perhaps mutt was confusing it. Regardless, I lost nothing, but messages now make sense.
[robg adds: Although probably not necessary given the intent of the hint is to remove them, you might wish to create a backup of the three directories before you rm -rf them ... just in case!]

