I found out today that anyone getting their PCM tuned using LS2edit, cannot get it tuned using any other tuning software and also you cannot get the PCM reflashed to the stock software by the dealer. LS2edit changes the security code in the PCM so it cannot be updated by anything other than LS2edit. This was confirmed by Carputing, makers of LS2edit.

Once your PCM is flashed, you cannot go back, you have to purchase another PCM. Be sure to discuss with your tuner and understand the consequences before you get your PCM tuned. Only LS2edit does this.