04 cobra warranty & sct ?'s

I know that if you have a sct flash on your computer that it will void the warranty, but if you return it to stock, can ford tell that you had it previously on? I thought I read somewhere that the computer makes a note of it and ford would be able to tell. Its an extended warranty, and I'll more than likely get any work done at a mustang only shop (was told any ASE shop would do), but would like to have the option of ford working on it if necessary.

Thanks