If you end up having no choice but to deal with duplicate, the "Mail Scripts" available on this page may be of use to you, I've used the dedup one to clean up some glitches that have occurred between Zimbra and Mail.app:
Andreas Amann's Freeware
When migrating to Zimbra (4.5.X, OS X 10.4), I was able to move one folder containing 10K+ messages from a local mailbox in Mail.app (also on 10.4) to Zimbra (IMAP) without any problems.
-rh