Hey brother I got a question, I haven't read second try
but how does your interpretation of Instrumentality work?
Are you saying she's gone in a physical sense? Or she doesn't exist anymore period?
Huh, okay...? Well, I'd obviously recommend reading it, though of course if you are following AcL, that'd be with a huge spoiler, given that
the mere existence of Aki and the presumed loss of her
was the main focus there. Not sure if you know at least the gist of it?
If not, basically, talking chronologically:
Post EoE, Asuka and Shinji remained the only ones left, eventually fell in/admitted their love, and - after some conflict over the unplanned pregnancy - had Aki and raised her for almost 4 years.
Then they suddenly found themselves peggy-sue'd to about Ep. 15 - without their child. So they use that "2nd try" to make things right (with more or less success), but always with the price in from of their daughter weighing on them. In the end though, turns out that after Kaworu's death, Aki also returned, found by Rei, who then, partially influenced by her and previous happenings, decides to dump Gendo's plans and tries to bring Aki to safety, while Shinji and Asuka are fighting. They win, Rei reunites parents and child.
So, post EoE timeline, Instrumentality would technically allow people to return - but either no one wants to, or they did few and far enough away that they never crossed paths - which would also go for Kyoko then, if she was in there. New timeline, Instrumentality doesn't happen - but in the final battle, Unit-02 self-destructs, so yeah, she's gone gone.
Which I admittedly kinda glanced over then, and is reason I wanted to rectify it now.