I had mine re-flashed and the tech did not provide any special marks to indicate it was modified. I think the only way to tell it has been done is to attach it to a computer such as the one used to perform the re-flash and examine the maps. I would not have the expertise to tell but someone more familiar might be able to tell. In my case (used Flash Tune) one outward clue is that the cooling fan has been re-set to come on at 205F and turn off at 195F, much lower than OEM. It think the OEM fan doesn't come on until around 215-220F? I'm pretty sure if the dealer figured out there was a re-flash and you had any kind of engine problem they'd try to deny warranty coverage. It should not affect claims on unrelated systems - brakes, ABS, etc..