Yeah, flashing as "module replacement" will effectively reset (erase memory of the permanent code) if people have access to OEM equipment. Then as APS said, you could turn off the codes (through HPTuners) before they set.
Couple of notes on that:
1. If you already have the newest GM update....GM does not recommend re-installing the same update (they put up a warning on the confirmation screen just before you give the final command)....but I have done it in a pinch....and it worked.
2. If you have flashed in a newer GM update/calibration with GM's SPS/TIS (than the one installed when you did your last tuning)................I would not just flash your last tune back into it. I would use your HPTuner set-up to copy the newest GM update/calibration to your laptop then open a compare file and copy changes from your last tune into the newest GM update/calibration....then load that back into your car. I think that will yield best safety for your module and best benefit from GM's improvements.