The following contains spoilers for Flashpoint Beyond #1, now on sale from DC Comics
Pretty much every DC concept that was reimagined in the Flashpoint storyline came out of it in a darker place. A grim timeline brought about by the Flash interfering with the past, this dark world was on the verge of ruin when Thomas Wayne was able to help the Flash reset the universe. But now that it's been mysteriously restored, those conflicts need to be addressed -- and in some cases concluded.
The Wonder Woman/Aquaman war that served as the backdrop of the original Flashpoint storyline is resolved in Flashpoint Beyond #1 (by Geoff Johns, Jeremy Adams, Tim Sheridan, Xermanico, Mikel Janin, Romulo Fajardo Jr, Jordie Bellaire, and Rob Leigh) -- albeit in a truly brutal manner.
At the heart of the original Flashpoint world was the global conflict that had erupted between Atlantis and Themyscira. In this timeline, Aquaman and Wonder Woman had originally been set for an arranged marriage, which would have united the kingdoms ahead of any conflict with the rest of the world. While Diana had developed genuine feelings for Arthur, his heart belonged to Mera. But before the wedding could be completed, Hippolyta was killed protecting her daughter. Enraged, Diana led the Amazons into conflict with Atlantis, eventually even slaying Mera herself. This led to Atlantis fully declaring war on her and the rest of the surface world.
This conflict served as the backdrop of the original Flashpoint storyline, with the climax happening during a climactic battle between these two forces. Returned to his world, Thomas Wayne discovers that the conflict ended differently now that the timeline had continued. The Amazons have been defeated, with Wonder Woman captured and prepared for execution. Aquaman even plans to turn his full attention to the rest of the surface world. Believing him responsible for the attack that killed Barry Allen, Wayne confronts the monarch and is quickly defeated. But Wonder Woman -- who Thomas had discovered and freed so he could claim her Lasso of Truth -- arrives at the battle and kills Aquaman while his back is turned.
In the aftermath, the Amazons are able to rout the Atlanteans -- and then announce their intention to claim the rest of the world, starting with Europe. It's a major shift for the universe, considering the scores of heroes who've gone missing or been killed already in the conflict. While Wonder Woman's actions do prevent Aquaman and his forces from sinking the rest of the surface world, it sets up her and her allies to turn their attention to man's world. This sets the stage for Wonder Woman to continue to play a role in the story, especially as Thomas tries to uncover who has been targeting him and prevent his attempts to undo reality again.
It also simplifies the conflict going forward, with Wonder Woman now poised as a more overt threat instead of being distracted by Aquaman's forces. The world is seemingly no longer at danger of being swept away by floods, giving Thomas (and the story) more time to uncover the truth of what has restored this timeline and why. The Amazons increasingly routing the rest of society would give a doomsday clock aspect to Thomas' investigation of what's happening in his world without stalling full-blown destruction needlessly -- as it would have had to with Arthur still alive.
The issue also continually teases this world's Superman, hinting that a confrontation between a dark incarnation of the classic trinity might eventually be in the cards for this world. But at least the survivors of this world can sleep easy with one of the world-shattering conflicts being genuinely resolved.