How CGC would handle it is a moot issue since the printed replacements are immediately being sent to the competitor for grading, and they stated that if the original lost books are ever found they would be destroyed. I think this is a very special one-off case and shouldn't be used to generalize, that's why as you said no one has ever seen anything like this before. A major grading company has never lost so many submissions with exclusives that a vendor could actually reach out and get indistinguishable replacements for (The books in question are mostly those that have the edition # printed on them like 24/50, 25/50, etc, so they're reprinting the edition numbers that were lost by the competitor)
But I guess just to go along with it, if they truly made it so its indistinguishable from the original print then what could they (CGC) do? It's like the pressing argument, even if pressing was considered purple-label restoration to CGC, its not detectable (if done correctly at least) unless its admitted to. The "2nd printing" would be undetectable unless someone told you it was the 2nd printing.