From what i know, the old ap v1, you could tell if the ecu was flashed. the v2 is a different story from what i know, something called the checksum value which tells you how many times the ecu has been flashed is the difference. When you save your stock data on your AP this takes a "picture" of the data before you flash your car, when you uninstall your ap it flashes that same data that was saved back onto your ecu like your ap was never there. I researched this a lot to and found out that info, others may chime in on that with their experiences and opinions.
When i was asking Cobb about this issue they said there is always a small chance that this could be uncovered but from the naked eye you could not tell, the tech or whoever would have to know exactiy what they were looking for to determine your AP was ever there