Iam Broke
Junior Member
I ran into this issue after replacing an ECU with another even though the new ECU VIN was changed in HP Tuners. The procedure below will let the car relearn VATS, but roll down the drivers window first unless you want to sit in the car bored for 30 mins. 
Disconnect the battery.
Change the ECU.
Reconnect the battery.
Turn the key on.
Let it sit for 10 minutes or until the security light on your dash goes off
then turn the car off.
Turn it back on sit for another 10 minutes or until the light goes off
then turn it off again.
Turn back on and sit for 10 more minutes or until the light goes off
and it should start right up after shutting it off one more time.
Make sure you DO NOT touch or use anything electrical in the car like the radio because its learning the PCM. You also cannot open any doors or anything.
If for some reason you swap ECU's again even to the original the procedure would need to be repeated.
Disconnect the battery.
Change the ECU.
Reconnect the battery.
Turn the key on.
Let it sit for 10 minutes or until the security light on your dash goes off
then turn the car off.
Turn it back on sit for another 10 minutes or until the light goes off
then turn it off again.
Turn back on and sit for 10 more minutes or until the light goes off
and it should start right up after shutting it off one more time.
Make sure you DO NOT touch or use anything electrical in the car like the radio because its learning the PCM. You also cannot open any doors or anything.
If for some reason you swap ECU's again even to the original the procedure would need to be repeated.