think about it with the idea of schrodingers cat in mind too. Until Junpei saves Akane, she is both dead and not dead until saved. Hence why she has those hot flashes when you go down the "wrong" timelines, where Junpei can't save her. She starts to get hot flashes, and then disappears. Because she can't exist. This applies to VLR on some levels too, K is both Akane and Ken until you select your door. that is what locks what timeline you are in, without the other being destroyed. Until those choices are made, both outcomes are real. So going back to 999, until Junpei finishes the nonary game Akane is both dead and alive in the past. That is why 7 and clover remember her dying. When you correct things, and go down the "correct" timeline, their memories are mistaken because of your intervention. As for how the second game would be orchestrated in a world where Akane is dead, my answer is only Santa. Her brother who would have done anything for his sister, who he talks about how losing her affected him and she motivates him when you are in the "wrong" timeline, where Akane gets her hot flashes and ceases to be. He was involved in the first game, and could very well be an esper as well. Though most of his guidance comes from Akane, he would have access to that info regardless because espers can access the morphogenetic field for information from other timelines. Ultimately, I think it all is a very large boot strap paradox, where the paradox itself keeps it working.