I think this thread is dead, but wanted to post something that I just learned.
I disconnected my battery and subsequently had all sorts of issues re-synchronizing my key fob with the alarm system.
After struggling with this for some time, I was able to synchronize my fob with the BECM again. There are a lot of procedures out there, and they were difficult to follow.
What finally worked for me was to follow these steps:
Make sure RR was unlocked. Press and hold the UNLOCK button on the fob while unlocking the vehicle. Return the key to the middle then let go of the unlock button on the fob. This procedure was completed in less than 2 seconds from button press, unlock with the key, center the key in the lock, then let the button go.
There was no indication from the car when the remote synchronized. The fob just worked.
I was previously trying to synchronize the fob by pressing the LOCK button on the fob while turning the key to the lock position. For some reason, that was not working. The UNLOCK sequence was the trick.