Many are way over thinking the AEM. If you are tuned, and not emissions deleted, there are two main options:
1. If you have a spare ECU, swap it out before the AEM, then swap in your tuned ECU after the AEM. Relax and wait for check.
2. If you do not have a spare ECU just let them overwrite the tune, then send the ECU back in to be re-tuned after AEM. Relax and wait for re-tuned ECU and check.
In the unfortunate event that your dash lights up like a Christmas tree post AEM, scream and bitch to have it fixed on the post AEM extended warranty. You drove in with no CELs and should expect to drive out without any.
There are a few uppity high and mighty folks who would impugn the integrity of the tuned who are participating in the settlement with the intent to retune immediately upon exiting the service department. I suspect most of them are from California and are envious and jealous of those who are privileged to be tuned. We can't tune, so therefore, you should not be tuned.
Actually, the settlement does state that the vehicle be emissions intact upon arrival for the AEM. Obtaining the AEM qualifies one for the refund. The tuned will comply with that requirement. There is no stipulation that one has to stay emissions compliant to retain the refund. So, the previously tuned are free to retune, or the untuned may obtain a tune if they so desire. Well, as long as they do not live in California.