[dnanian]

Well, John, I don't understand how that folder can vanish. Truly, we do not ever delete files from the source. I can see how, when combining backups, you can end up with a problem (Smart Update of one drive will remove what you copied from the other).

But, the *source* should never have files removed.

I guess I'd need to see your SuperDuper!.log. If you could locate it (it's in Library/Logs off your Home folder) and send it into support, I'll take a look and see if I can figure out what's going on.