Programming the key is the issue, or should that be the security chip in the key. When we received our second remote key, we did not have the blank key with us, so it became a useless piece of junk, other than it would unlock doors and set the car alarm off. In other words, when a new key is acquired, all keys need to be linked and programmed along with the security system on the car.
Now, months later,,one of the remote keys failed. Not the remote itself, but the chip in it. As a result it would not start the car. The motor would turn over, but the car would not start. A replacement chip was ordered and placed in the existing remote. At this point, we took all three keys in to the dealer and they were all reprogrammed along with the non-remote key and of course the cars ignition chip.
I would say that a way would need to be found to have all keys and the security chip in the ignition reprogrammed at the same time. If a locksmith has this sort of equipment and knowledge, than great, but I think you may find it's a job for the dealer.
Now, someone with electronic knowledge may want to refute what I am implying from my experience, but that is the way I saw the experience first hand.