Piltdown Man,
Not to flame you or anything, but it is up to the manufacturer to keep the derivative aircraft off the existing Type Certificate. If Boeing elects to keep the 747 Advanced on the existing Type Certificate what has already been certified will be grandfathered.
All aircraft manufacturers want the ability to claim equivelency to past work so they dont have to pay to do it again.
Even you say "re-certify" in your post that I am speaking to.