On another note, I just went back and reread the 'Superman Reborn' arc, and I can't help but think the merger of Superman(and his continuities) is what Mxy intended all along.
After all, Mxy was pissed that Superman didn't come and rescue him after Mr. Oz's failed kidnapping --he thought Supes had forgotten about him-- so he set out to make things how they were in the 'old days'. I mean, Mxy's previous encounters with Supes(both pre-Crisis AND pre-Flashpoint) were shown to be some of his all time favorite memories... And what better way to get Supes to remember those 'games' than to merge said continuities..?
Why else would Mxy specifically take Jon to a place where he could access/manipulate both iterations of Superman? Mxy didn't necessarily seem surprised at what Jon did, after all, and there's no f*cking way he didn't know the 'Superman-orbs' were there.
I think it was all part of Mxy's plan, tbh.... His greatest game with Supes yet.