From my experience, HP can overwrite a ford performance tune. I put a stage 2 power pack on my 17 mustang GT, and after I installed the long tube headers, I had to take to a local shop to get the CEL turned off. HP tuning software was the only one that could access the FP tune to modify for the header install.
Also, if you buy the FP tune, download the file from ford yourself and give a copy to the tech at the dealer on a thumb drive. DO NOT let them download the file. Several people in the mustang world let the dealer download the file and they got screwed by the tech. They either kept the file themselves, and in one instance I heard of the tech deleted the file from the dealer laptop after the install and now there is no way to go back to stock.