I always contend there was a way better way to do that. You do with Superman and Lois what you did with the rest of the verse. Reintegrate the history you want back in. With Jon, you pull almost an inverse of the Dawn scenario from Buffy season 5. This kid just shows up. He has memories of being Clark and Lois Lane's son but no one else does, namely his own "parents". You play with that mystery, inviting the question if he's even real or not, before revealing that he is indeed, and Superman and Lois don't know of him because of the whole missing ten years plot point. He then is that buffer shedding light that the timeline is wrong, speaking of a more Pre-FP reality. Why does he exist when the missing ten years didn't originally include him? The same reason fixing Zero Hour resulted in a guy named Kenny Braverman existing. Comic book reasons. And why is he brought back before the memories are returned to his parents? I dunno, Mxy did it somehow. That vague answer worked well enough for Reborn as it is, lol. Speaking of which, an equivalent of Superman Reborn then restores their memories, and in effect introduces us the audience to those memories. At this point Clark and Lois are married again as they were before and Jon is included in that status quo. It requires putting the family dynamic on hold for a while of course in favor of the mystery element, but in the scheme of things you're not losing THAT much time before you get to start to build it in earnest, and in the end it would have resulted in a little less of a jarring situation, and I think it would have left New 52 fans feeling far less rejected than killing off the entire version did.