I took my truck into the shop the other day for intermittent stalling and hesitation. The service manager told me that he would order a throttle body and reprogram the PCM.
I am not sure that he has reprogrammed the PCM. Do the keys also need to be programmed when they flash the PCM?

 

I had a reflash for the "check engine light" and the "wrench" light on at the same time, problem fixed, and they did not ask for my second set of keys. Both sets still work.

 

No. The key memory is not kept in the PCM. It uses its own module.
So not to worry.

Mike