I dunno about with diablo but it does happen. That is why they generally have the ability to backup the stock tune.
SCT is awesome in that if you brick your car they can take the stock tune and build a recovery file. I had this happen once and that fixed it.
You switch tunes enough it is bound to happen once. Exact reason I don't change tunes on the weekend while SCT is closed.
MustangEvolution ROCKS MY SOCKS!!!