They can probably tell if it's been flashed...and while Magnusson-Moss says they have to prove it, if it comes down to Ford and their lawyers vs you, good luck. I think the last person I'd want to go against in a courtroom is a lawyer with an engineering background (come to think of it, maybe I'll go get a law degree when I retire, that sounds like it might be fun).
Also, with regard to flashing it back...or understand before you tune that it's pay to play and just own it if something powertrain related fails.