First I'd want to know how many keys can be coded to the car, some car makers can have 3 and if this is the case with VW I'd want all 3 just to be sure nobody has the 3rd key.
When keys are coded to current VW models only keys present are coded to the car, so any previous keys are removed from key memory.
So in this case, both previous keys would no longer work and only the one, or pair of new keys coded at the time would work.
Keys are 50% coded from factory as they are ordered to chassis, and when they arrive at dealer they are then 50% coded to match up with that car. The key can only be coded to that car and would not work if attempted to code to any other vehicle.
Worth noting if keys have been lost, I would also request that the remaining lockset is changed. On a 7.5 GTI the only physical key lock is the passenger door, the existing lost keys would fit in the ignition barrel (you could request this is changed but would involve much more work, not worth it IMO) but would not start the car as they would have lost their coding to the car.