Is the key in the ignition when you try to charge the battery? If not, try putting it in, BY ITSELF (no other keys on the ring) and make sure the key ring is not hanging over the key itself. See if that works and let us know.
I can only find procedures for coding new keys---not sure why this is happening but obviously your key is not being recognized for some reason. You might ask the dealer's service department. Lexus service is often quite helpful. Worth a shot.
I wonder what would happen if you took the battery OUT and recharged it?