awu_gigabyte,

I was worried about the same thing, I have to get my truck NY State inspected in June so I went back to stock tune about three weeks ago and my truck was showing P1000 code, I removed my Edge for the time being, after two weeks it still showed P1000 so I was a little bit worried, well today I checked the code with my Edge again, temporairly plugged it in and the code was cleared....
I might be wrong but I think that every time you change from stock tune, #1, #2, #3 or back to stock tune, it resets the computer and causes the P1000 code to be set again and the computer has to relearn.
The problem with the NYS inspection is they plug a cable into the diagonstic port on the truck to check for any codes and if it has one it won't pass inspection, the service facilitys computer is tied into NYS Department of Motor Vehicles system and any vehicle from 1996 and newer must have this done......
I don't know if lets say I had my truck set on tune #2 "Towing Mode" with no codes if it would pass inspection or not.......???