Any tuner worth their salt can set the observable value back to 0 or 1 for the flash count. There are traces deeper in the ECU that are detectable by deep diving the ECU, which is done on some high-cost or abormal warranty procedures. No flash tune is undetectable, period.
Take this with a grain of salt, as this is what I heard based on third party hypothetical logic (Bro science).
When you first install the Cobb AP, it takes a snapshot of the ECU parameters (Flash counter etc). Once unmarried the snap shot is pasted back onto the ECU as if you had not flashed at all. Parameters are reset to what they read prior to marrying the Cobb. On a hypothetical assumption, this would hide all the increased tuning parameters, such as boost, timing etc). which is why it takes 30 minutes for the initial marrying of the AP.
I don't remember where I read this or who told me this, but I have been told this before. Whether this is true or even possible, I have no friggen clue LOL. Disclosure: **I have no knowledge of how ECU's work flashing back and forth**
The AP flashes differently than the other tuners based on what I have read and this method potentially hides the ECU parameters (better?).
Please don't flame me, again I'm just passing on the "logic" I've heard.
I for one **DO NOT** think it is possible to hide from Odis's scan when unmarrying the AP back to stock. But I would LOVE to be wrong.
NeedmorePSI went in for warranty work for his intake manifold after unmarrying his AP. I would love to hear back from him to see what happened if they scanned his ECU and flagged him TD1. But from what I've seen, I think his manifold was replaced under warranty (will need to confirm).