[RocketSurgeon]

I recently bought and restored a repossessed 2012 528xi. It only came with 1 key, and the other one was in the hands of the previous owner. I decided to block out the missing key to avoid any problems. I went into ISTA+ and went to the block key menu. The program checks the current key number so you cannot block your current key! So everything was working perfectly with comfort access, remote, etc up to this point. ISTA does the search for the current key, and says it cannot locate the current key number, so service function will be terminated without blocking any keys. So I pull a spare key battery out of my bag and replace the key battery. Now remote and comfort access don't work! I can only open my door with the key blade, and can only start the car by holding the key to the side of the steering column. 
I have tested the following:
Key battery registers 3.3 volts and key outputs a 315mhz signal.
ISTA+ shows no error codes of any kind, and CAS/Key troubleshooting finds no faults.
ISTA+ remote test correctly displays lock/unlock/trunk/panic signals from key, and strong key battery.

So the key is putting out a signal and the car is receiving a signal, but remote and comfort access don't work.
I tried a battery reset, etc without luck. Holding the key to the column allows me to start the car, but does not enable wireless features. Key 2 (my only key) shows as enabled.

What happened and how do I fix it? Did something go wrong with CAS, or did something get corrupted in the key during battery change? Thanks in advance.