Ford Puma Infra Red Type Remote Key Question

My infra red key won't lock / unlock the doors remotely. I've changed the batteries (in well under the stated 15 seconds), but before I try reprogramming, am I correct in thinking that the transponder in the key - that 'handshakes' with the transceiver in the ignition switch - is completely separate from the programming of the key. In other words, if I get into a pickle with the reprogramming ritual at any stage, I will always be able to start the engine? Thanks for any responses.