Now, what I don't know the answer to is what happens if the details on his new ATP JAA certificate doesn't match the details on his existing FAA 'on the basis of' certificate
Unfortunately this renders the FAA "based on" ticket invalid. My mate had this problem after he got the JAA CPL - then went to the USA to fly on his "based on" ticket. Didn't work and he had to go through the validation process and get a new based on ticket.