I am having the same exact problem--I originally moved some messages to a non-synced folder, turned-on the sync, but now those messages don't show up anywhere (in my web-based Yahoo mail). I tried moving them back to the inbox but they still don't show up either (only in Zimbra).
Anyone have any ideas how I can get those messages back?
I've tried moving some test email messages after, and the same thing happens whether the folder is synced or not.
[Update]:
I just checked my mail in Zimbra just now and it seems like the messages I moved with Zimbra now show up in my web-based Yahoo. So it's all good now

Rorym you should check to see if this problem is gone, hopefully it is.