I have been having some trouble with one of my mail boxes in Apple Mail, probably caused by connecting it to my Daylite contacts. Yesterday I found this neat trick called Rebuild. I thought, cool, it will fix all my problems. NOT!
Rebuild deletes all emails that are not on the server. So for me, it removed all my emails, and I do mean all of them. Luckily, I have copies for most of them, but I still lost a lot of old emails.
DO NOT use Rebuild unless you want to loose all those old, unsaved and un-archived emails.