Another update.
I dug deeper into the mailboxes - and found the "subscriptions" and actual mailboxes weren't correct in all cases. I guess when I shifted to the explicit INBOX/ namespace not all the existing boxes migrated correctly. So...after manually correcting all the "subscription" files, and manually moving the duplicated "Archives" folders to the correct locations nearly all the errors have gone.
I wish I'd gotten more inforrmative error messages, and processes certainly shouldn't have crashed, but since I obviously created the problem due to manually poking things and improper configuration I guess I can't complain too much.
I still have problems using the "-N" flag for syncing - but things seem to be working with the multiple explicit "-n" namespaces. I do still have the locking error appearing during long-running syncs - I don't see why Dovecot doesn't know that it's already syncing a given user before trying to start a second process. Probably something else I setup wrong but I don't know what.
-- Daniel