My ac died temporarily after a reflash. No physical changes to the car. The "fix" was putting it in defrost mode. Hasn't happened since.
You probably just need to retrain the limits.I'll have to look out for this. I just installed a quick shift and removed my battery. But the only thing I noticed not working was the one touch window up and down.
I believe you need to manually roll the window down all the way and back up all the way a few times. Then it will do the auto down and up again.