I had the same issue changing from a auto the manual calibration on 2010 Camaro. The changes to the drive by wire software caused throttle to stop responding if you just flashed with TC OBD2. I think now if you try to full flash with a .cal, the software will tell you its in-compatible, and will not let you flash. I have GM MDI and GM TIS to flash for application with VIN, then use the CAL. This explains it a little more, this was email from John at TunerCat.
"This can be a problem if you are switching applications with a particular ECM. There are 8 calibration modules in these calibrations. Modules 7 and 8 are used by a secondary microprocessor in the ECM and are not typically used in the calibration process. These modules are not read, modified or reprogrammed by the WinFlash OBDII program so the program will not allow you to program an ECM with a particular calibration file if the modules 7 & 8 associated with that calibration are different from the modules 7 & 8 that are currently stored in the ECM.
The GM system does reprogram modules 7 & 8 so you can change applications using that. SO what you'll need to do is reprogram the ECM with the stock calibration that you want to start with using the GM system. Then you'll be able to tune it with the OBDII Tuner program.
Best regards,
TC"
At the time, TunerCAT OBD2 was the only software that would warn you and prevent you from programming. HP tuners would freely flash calibrations in the PCM regardless to if the modules 7 & 8 matched or not.
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