WMG / New 52

The Apokalips invasion was an incursion into every universe at once
The 52 remaining earths are the only ones that were able to repel Darkseid's forces. This will come up again in another arc (because, of course, you can't keep Darkseid down for long).
  • As a result, each Earth has one of the New Gods of Apokolips stuck on it: DeSaad on Prime Earth, Steppenwolf on Earth 2. At some point Darkseid will reassemble his forces to attack the worlds again, and the heroes will unite across universes to fight them.
  • Earth-23's Apokoliptian refugee was Glorious Godfrey, After the invasion, he ran for US president against Calvin Ellis, under the name G. Willard Godfrey. (Because if your hero is Super-Obama, your villain is Super-Romney, right?)
  • Earth-8's refugee was Grayven. Control of his army was usurped from him by a trickster spirit, but he has rebounded magnificently, scouring that universe for cosmic weaponry while he searches for ways to stalk Death of the Endless.

The original universe still exists.
We already know there are at least three universes. The old one has to be out there somewhere, right?
  • We know from the old 2000's Superboy series that, somewhere out there in Hypertime, Earth One still exists.
  • Confirmed in a sense. Pre-Flashpoint Gotham City exists in Vanishing Point, along with cities from pre-Zero Hour and pre-Infinite Crisis

The "Dark Supergirl" personality has been in control of Supergirl ever since Flashpoint
Admit it, it would explain a lot.

Flashpoint Never Ended
  • In Flashpoint, Barry Allen's memories began to change the longer he stayed in the Flashpoint universe. Now count how many times a single character's origins have been rewritten since the New 52 began. It seems likely that history is constantly rewriting itself so that it can accommodate an increasingly chaotic present.
    • Superman also had a dream of a life that strongly resembled his Post-Crisis years, complete with his step-parents alive and Lois as his wifely
      • Unfortunately by Convergence and Rebirth, which have introduced and have the Post-Crisis Superman the spotlight back. while New 52 Superman has been sadly pushed aside as a mere imposter.
  • Also, take into account that Batman has only been active for about 7 years when his 10-year-old son dies. This could be the universe ironing out one glaring inconsistency.
  • Now The Flash has to contend with a future version of himself. How well could he have fixed the universe if he has to kick his own arse?
    • Jossed The Flashpoint version of Gotham City has been captured by Brainiac and preserved in Vanishing point.

Wesley Dodds is having a dream
In Sandman Midnight Theater, Wesley Dodds encountered Morpheus the Dream King in his glass prison. He's still standing there, having an extended vision.

H'El is actually Superboy-Prime
My train of justification: Superboy-Prime was a Kryptonian from a destroyed iteration of the multiverse. He survived which his ludicrous powers intact, to continue on in a world that he had no place in. He carved the shield of the House of El into his chest. Theoretically, he could survive the destruction of that universe, because it was never his.

H'El, meanwhile, is a Kryptonian with no apparent origin, trapped in a closed chronal loop, which ridiculous powers and a (reversed) El-Shield carved into the skin of his chest.

If Superboy-Prime survived Flashpoint, he would be shaken, buffetted, but still dangerous. By trapping him in a closed chronal loop (his two appearances apparently feeding into one another ad infinitum), the universe has saved itself.

The entire New 52 was orchestrated by both Zooms
The last time he was seen, Hunter Zolomon (the second Zoom) approached Eobard Thawne and said they could make each other "better." Now, his whole shtick is about making "better heroes" by making them experience tragedy; so he and Thawne somehow manipulated the timeline a la Flashpoint to make the new timeline work their way. Plus, we haven't heard anything of Zolomon since that last appearance of his, so...