If the person who sold it to you did not return his car back to stock using the handheld SCT before selling it to you, then it gets a bit more pricy.
But anyway, yes they will clear the files and you will pay them to custom dyno new files for you on the spot at a Mustang shop or you will have new files created through AM and BAMA for you to upload and start using.
Pain in the *** at first, maybe, but worth it all in the end.
Call AM/BAMA for free answers.
'97 3.8L V6
1996 SVT Cobra White