When I initially set up my mail server and transferred off my old courier imap server I got duplicates with imapsync. I'd check and see how your emails are syncing. In my case I had duplicates of all the folders inside of the Inbox as well as outside of it. It made a difference in the size for sure.
Also, I have been working on a way to do individual account syncs for the purpose of archiving. It moves the whole user account, calendar, mail and all. Well, all except the user account data, things like address, name, and such.
Mail | Dell 2950III | 2x Quad Core 5420 | 8gb RAM | 6x 146gb SAS RAID 0+1 | Red Hat 5.3 | Zimbra 6.0.10 Network Edition
Test | VMware ESXi Whitebox | Phenom II Black 3.2ghz | 12gb RAM | 6x 1tb SATA RAID 0+1 | CentOS 5.4 | FOSS, Not in use now