ManofSteel1979 summed it up pretty well, but I should have clarified in my post: since I am a trade-wait guy these days, I have not yet read the Rebirth Superman or Action Comics outside of the Rebirth specials and the first issue to follow in each title. So I don't know if Superman remembers that event or not. However, as MoS1979 stated, up to the moment of Flashpoint it had been retconned. If I recall, Superman even dreamed about it once after Infinite Crisis. He woke up from a nightmare and said "Lois? Have....have I killed?" Her answer: "Of course not!" (paraphrasing)
So, the Superman who appeared in Reign of Doomsday and The Black Ring (the final 2 PF stories) did not have killing Zod as part of his history. The Superman who appeared in Convergence, who I have every faith is the same guy as before Flashpoint, also did not have that history. Ergo, until they state otherwise, I will assume Rebirth Superman doesn't have the history of killing Zod & co.
Again, that event still happened, and the fallout stories as well. We remember them. Superman does not. Zero Hour, Birthright time tunnels & Alex Luthor / Superboy Prime changed history, and Superman's memories changed with them. That's how I interpret it, anyway.