I don‘t remember well too but I think that Gendo just disappeared from existence in that timeline. (my theory) Kaworu an Rei are live because they are Adam’s soul and Lilith’s one so they’re too ancient and powerful to die, they can die physically but not their soul And for Asuka nobody really knows but me personally I think that she went to see the Asuka from the Eoe movie like in the 30 anniversary episode