Could you just reload your original factory tune for the inspection? I just received my registration renewal today after loading my custom tune for the first time a couple of days ago, so I'm interested in this too.
Not sure how Colorado works, but you most likely just need to make sure readiness monitors are set. Takes a few drive cycles to reset after flashing, battery disconnect, etc... you can usually read them with a code scanner. I have an OBD-MX bluetooth scanner and use their free phone app...shows readiness monitor status.
Only people who MIGHT have issues are the Cali people since Cali has said they are going to interrogate the ECU and make sure you have the factory flash on it. Not sure when this bit of genius is going to start. Guessing if you dont have the factory flash, but what you have is CARB certified, you just show them your stuff and be on your way.