Mail App Restarted Itself
So basically, it seems that on OSX 10.8 mails are not longer stored in

~/Library/Mail


but in 

~/Library/Containers/com.apple.mail/data/Library/Mail/V2


If your mail app restart / restore itself unexpectedly simply copy the folder called "v2" from one location to the other and restart the Mail app. 

Everything should be restored.