Have you actually looked in your profile to see if the mbox files are still there? They should be somewhere under Mail, perhaps under Local Folders with the name of the folder.
If you're lucky, SM just lost track of them and they can be saved. I'd suggest first making a copy of your profile and then looking for the missing files. Sometimes it is just prefs.js that got damaged and restoring that from your backup will restore stuff. Other times it is the msf files got broken, they can be rebuilt but you may need to recreate the folder, shut down SM, copy the mbox file over new one, restart SM and click on the mail folder, open the properties, and click fix folder or such.
Frequent backups are a good idea, even keeping a couple of backups on your hard drive as often something like you experienced happens. I've had prefs.js get zeroed out, and profiles.ini likewise get zeroed out. Both very easy to restore.
