I'd dissagree. I think you should tell them the truth even though they'll charge you time to diagnose the code via Vadis. I'd have to assume that the warranty is up or one would have taken the car to a dealer for the CCM in the first place as it would have been fixed for free.
Another reason to "fess up", technically a new CCM should have SW DLd to function correctly. I'm surprized that it works w/o new SW now.
Telling the dealer the truth will prevent them from guessing that other faults might exist from the codes now stored, thus preventing misdiagnosis (assuming that the codes lead to a real problem). If you tell them the truth, they'll just read and clear the codes w/o looking further for possible problems.