I wonder what it would be like--to be the fastest man on Earth? Well...I'll never know-- The Flash was just a character some writer dreamed up! -Barry Allen (showcase #4)
I just looked at the panels again and it seems like John willed Red Lois and Clark being actual physical presences while Blue Clark and Lois got thrown off the panel. I don't think they have merged at all. Take a close look. Nothing shows that John even touched his mother and father. So something isn't quite right.
As I've written in other threads, I don't see why a merger is such a difficult concept to grasp or for the creators to establish.
We don't know the how/when/why (though we can speculate most on the last), but Superman and Lois were divided into two beings. This likely happened at the moment that a number of forces were working simultaneously to affect the timeline: Barry, Pandora, Brainiac, and possibly Manhattan and/or Ozymandias or whoever Oz is.
In the process of this manipulation, Superman is divided in a similar fashion to his previous division years previously. Essentially, his energy and essence is divided, with Red being used as the post-Flashpoint Superman and Blue remaining pre-Flashpoint Superman on Telos. Due to her strong connection to Clark, Lois is also divided.
Blue and Lois are returned to what they think is an alternate Earth (it's actually just altered) and go into hiding with Jon. Red and New 52 Lois go about their lives.
After Reborn, Red and Blue and both Lois' are merged, though this merger retroactively affects the timeline. Where once there were two Supermen living in different dimensions with different experiences, there's just one. I don't even think this post-Reborn continuity will acknowledge New 52 Superman, just some of his adventures.
Here's what I mean:
Clark is raised by the Kents, who live until his death. He's friends with Lex, has a relationship with Lana, and at some point, meets the Legion. He travels to the future and operates with them as Superboy. Once out of high school, Clark goes to college, travels, eventually moves to Metropolis. His first job is now at The Daily Star, he becomes close friends with Jimmy, and is a rival with Lois. As Superman (perhaps in a proto-costume), he has adventures with other heroes, including Diana. They date briefly before Clark realizes he loves Lois. The Collector of Worlds/Luthor from Morrison's arc can also fit in here.
The rest of Superman's history unfolds as it does post-Crisis. Clark reveals his ID to Lois and eventually proposes, dies fighting Doomsday, returns, they marry, Red/Blue and other stories up to New 52 happen.
A few years later (in DC time), things can go in two directions. A: Clark and Lois are abducted by Brainiac and leave other heroes like Steel to defend Metropolis. Lois and Clark eventually return with Jon. OR B: A split happens when Brainiac takes them, creating the New 52 Superman and Lois.
I suspect the new, post-Reborn timeline will be in flux and will not be a fully merged timeline until the end of Rebirth. This would mean that Lois and Clark would retain the memories of their other selves, which could lead to some fun stories in the next year. Action Comics #1000 hits, is an integral part of the Rebirth climax (it's going to debut at the end of March 2018 unless there's a change in scheduling) and the result is a new, merged timeline that will then become the template for the new, post-Rebirth DCU.
Make no mistake, though, that no matter how it happens, there will be a point in a year or so when there will only have ever been one Superman who has gone through all of the events we've been trying to reconcile here. There's no way that DC will leave this convoluted narrative in place after the culmination of a two-year, line-wide event designed to restore previous continuity as the basis of a new continuity that has elements of the New 52 mixed in.
What a difference a year makes. I still believe everything I initially said, but well, what's happened has happened, lol.
They can be a great people Kal-El, they wish to be. They only lack the light to show the way. For this reason above all, their capacity for good, I have sent them you. My only son. - Jor-El.