Someone with an aftermarket tuner could reflash it.
I've never heard of a tune going bad. Are you using the same mechanic? Maybe some of the other guys here have seen this, but I'd get a second opinion, which the dealership will probably give you. I'd be more inclined to believe in an electrical short from the PCM. If you knew all the work your mechanic did, instead of just his conclusion, that would be way more helpful. Like your algebra teacher said, "show your work for full credit."