There's two functions of the key fob. One is the central locking and the other is the immobiliser, so when you say that the car doesn't register the fob, what exactly do you mean?
I know from memory that P0AFA is Hybrid System Voltage Low, so check that you've connected the voltage sensor back up correctly. Also check that the Service Plug Grip is replaced correctly.
You say you managed to scan it "with proper software" - was that Techstream? As far as I know, Techstream is the only one that gives the sub-codes as well as the main codes and this is very important. If you look at the screendump below, you'll see that P3004 covers six different problems and only the sub-codes differentiate them for you.