Originally Posted by Csinclair1991
From what I was told is the engine is trying to run the tune on the factory settings
I'm not completely sure of your situation, so if you could provide a little more info that would help. That being said, if your Mustang had a custom tune uploaded to its PCM, it's physically impossible for the PCM to revert back to the factory settings. Those settings are now longer available to reference once a different tune is uploaded.
I would talk to the shop and have them clear the situation up with you a little more thoroughly. If this is what they're truly claiming, then I'd get a second opinion at a reputable shop.
Hope this helps!