The law doesn't require you to have a stamped in Vin number, I asked the DVLA a while back about how to go about repairing a sill that had extensive rust & was very close to the Vin number. They said to take numerour High resolution photos of the repair at every stage (they said I couldnt take too many), so if you used the same colour shell and made the photos tie up then you could do it that way.

They said to repair the area with fresh metal and keep the stamped number section safe if there was ever any doubt.

It's conceivable that a sill could rust near the number, so as long as you have evidence and photos to proove you have done a repair rather than a re-shell then it's fine

Dan