Andrew snapped out of the persona and had a moment of clarity and found out his dick was gone for good and the pussy was real. That shock might have nuked some memories.
I think this really depends on how you interpret some scenes (totally understandable given the theories and the non-linear story so far).
We've basically been told that there wasn't a separate persona during the timeskip. Apparently the timeline goes:
Andrew gets the first set of major surgeries (prosthetic). He speaks with Marina and they come up with a safe word. Andrew decides to behave as Elena and convinces the entire family to do this.
For a while, Elena behaves perfectly in character. At some point, the family has her go through a second surgery.
Elena has lost her memories of a certain chunk of time.
For a while, I think we were speculating that the memory loss was another personality "at the wheel", but the later chapters and especially Elena's monologue explaining everything seems to be contradicting that.
Basically, I don't think we have 2 sets of memory loss: as in, we don't have memory loss due to another personality and also memory loss due to shock. I think we have one or the other. This would mean that if there was a "shock", you'd have to explain two things:
1) Why wasn't Elena so shocked over the first set of surgeries? I mean, she was flat out told she'd been castrated and although her dick was "hidden", I mean... you're still waking up with what seems like your penis gone. But that's less important compared to...
2) Why would Andrew consent to be further feminized and then find it shocking when he was? Or why/how was Andrew knocked out and forced to undergo more surgery (specifically in such a way to explain the family's later reactions that I outlined in my previous post)?
Just a minor clarification before we go down a rabbit hole of implanted sci-fi organs: "Elena" is already past the age of menopause so it wouldn't make any sense for them to make her capable of pregnancy. I'm pretty sure Nikos was just gaslighting her to make her believe that she is the biological mother of Eva and Sofia (and/or to create an alternate reality per @LadyBoyJay's theory).
Sure... although, would it really be out of character as an act of control for Nikos to want to impregnate his wife? Given how they seem to be trying to recreate the marriage again (proposing, having a marriage, etc).
That said, I'll note that I brought up the lab organs point not to say that I think the story is going to go down a pregnancy route (although it wouldn't surprise me if it did), but more so to say that I think we've got some futuretech medicine here. She might not necessarily have a womb and ovaries, but the whole emphasis on "real" and now all this pregnancy talk (alongside a second surgery that was able to be snuck in) just thematically feels like to me that there's something beyond our current medical tech.