I just had my local shop call Cobb for me while I was at work. If I buy the AccessPort directly through Cobb I'll be eligible for a full refund if the AP doesn't pair to the ECU correctly. I'll call them directly today for further details. I don't want to go through Cobb as they weren't able to crack VVEL, but so far there is no other alternative to going back to a fully stock tune with the other methods.
UpRev, Technosquare, etc. will all leave their tunes on the stock ECU and can be found if the dealer does a thorough enough check. Basically if there's a major warranty issue that comes up they'll find the aftermarket tune.
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