Will this cause any problems with seen / unseen flags (or anything for that matter)?
Seen flags are kept in a different database, under /var/imap/user/X/user.seen. I presume Cyrus gracefully deals with nonexistent folders in the seen/sub files, but I haven't looked at that part of the code so conceivably that might be a problem.
If you want to be sure, restore the missing directories from backup and delete them the proper way though Cyrus.
-- John A. Tamplin Unix System Administrator Emory University, School of Public Health +1 404/727-9931