[spoiler] um...Could we not just have come back for him?

[WALP]

Well, she would've had to see Simon-2 suffer after waking up in confusion and learning that they're all doomed. I'm sure she wouldn't have wanted him or herself to experience that, especially because he would've probably started blaming her for everything, just like Simon-3 did.

It's definitely the explanation that makes the most sense, but her angry reaction to Simon-3
after launching the Ark, implies she thought Simon-3 understood the copy concept by now, so if Simon-3 can deal with, why should Simon-2 not be able to?