Since the AP overwrites the values inside the ECU and the tables become whatever we change them to, there is no way for the ECU to go back to stock unless you flash it (re-write) back to stock.
The adaptiveness of the ECU is not confined to the Mazda ECU but OBDII ECUs in general. This adaptiveness is the bane of offset devices (piggybacks). Essentially with a piggyback you want to alter the value of a given load point inside the ECU. Let's say IDC (injector duty cycle) at 4,000rpm is 50% just for argument's sake.
Now, we have a bigger turbo or we increase boost pressure, we have to increase IDC at that load point by 20% so we tell the piggyback to add 20% to that load point. Now, the ECU sees that at that load point, the car is richer than it should be so it decides that at our load point it is going to cut IDC by 20% to 30% IDC. However, our piggyback is still adding 20% and you are back to an aggregate of 50% IDC, your ECU has just "learned" around your piggyback.
Since the flash that is loaded into your AP is a new ROM for the ECU, these values cannot be "learned" around as they are written to the ECU. The AP unit itself is a delivery system for the ROM as well as a data-logger, scan tool etc.
Hope that clears some things up.
Travis
COBB Tuning