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So this debate happens on just about every enthusiast board. What I know personally for a GR/GV STI... I know of a car that had the shortblock replaced under warranty 3 times, you better believe they checked the ECU before authorizing each replacement, and each time it checked out - they pulled the CalID/VIN to verify. It ran a Cobb AP and unmarried it each time before taking it in. The Cobb AP works in much the same way the OFT does (from my limited knowledge), where it rewrites the factory ROM back to the ECU when it is unmarried.
The same debate is on the STI boards about whether the dealer can tell or not. I think if the car is brought to the dealer running a different tune than factory, they can tell (some people probably bring it in or don't unmarry properly or run something like ECUTek). Cobb has a "stock" tunefile that isn't actually stock but is "like stock" that the user can switch to quickly with the AP, and maybe that's where some confusion came from.
There are other clues that might lead a dealer to suspect whether it's been recently flashed, like emissions readiness, but driving a few miles after a reflash would eliminate that, and apparently it's the same artifact as if the battery power was reset, so it's not conclusive.
It won't help things if there is physical evidence that a header/downpipe/intake/whatever is/was modified.
Of course if they have evidence of you tracking/autoxing (FB, social media, google your name), then you're F'd, ECU evidence or not.
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