Wow. So does that include all alien lifeforms as well? Or did they get left behind, making humanity alone in the new universe?
Alien life with no future potential to become beings with their own Well got copied. Alien life that had their own Well of the Furies containing their future potential would have not been copied in all likelihood.
Of course, with cosmic events such as this, there is always the possibility for exceptions, if someone wanted to explore that possibility. This was all orchestrated by RulaCole: RulaCole could have made mistakes, he could have lacked the power to perform the task perfectly, there could have been other powerful entities that refused to go along with the cosmic rewrite, etc. The narrative is that humanity is now free of outside forces that could control its destiny, but a) its unclear what happens to "god-like" entities that were a *part* of humanity's destiny and b) its unclear what the rules are for a version of reality that exists only within the dimensional plane of dreams.
The fourth-wall point to the story is that we can speculate, but we cannot be 100% certain what is happening to our characters because we can't reach them anymore. In-story they are free from outside meddling from the Battalion, out of story they are also free from outside meddling from us, until someone figures out how to allow us to regain contact with the game.
We can, of course, dream about them.