I went with "Hard reboot to a singular Superman throughout timeline" even though I don't actually want another New 52 style reboot. Just do some kind of comic booky thing where the Supermen and Loises are reunited and we can continue forward with a recognizable status quo. With or without Jon doesn't really matter to me, but you can't remove him now without making the character arcs seem artificial in the same way "Brand New Day" messed with Spider-Man. So keep the son and retcon everything so there's only been one Superman.