One option would be to export the files from ZD and take that and import it using the ZWC. You might wind up with unwanted folders (such as the Outbox) but at least you'll have all your stuff back in the server... I'm thinking this would have to be done on a per-user basis.
Another option would be to use something similar to the methods found on the wiki under
Mail Migration to do it. But this is a shot in the dark, I've never tried it and can't guarantee it will work.
I don't know how this will affect the following sync back to ZD. You might end up with duplicate messages on the desktop.
My ¢2