"I can think of no reason you would EVER want to turn off the transponder once in flight, and I think that we will find this option is rapidly removed from the flight deck.. "
The time mine started squawking 7600, despite what it was set for, in the YYZ control zone comes to mind
14k hours and never had a transponder squawk something that I hadn't set (deliberate or as a mistake). Besides you've got two... Switch it over to the other one. HIGHLY unlikely that both would be buggering around... The point stands..