I'm sure it's the same as the passat, so in order to synchronise the key:

1. press the unlock button on the fob for one second
2. open the door manually with the same key

The car recognises the mechanical match and syncs it with the car.

The other key that unlocks the car might not have a transponder chip. You can get a virgin one from ebay but you will need someone with vagcom to pair all keys again at the same time.