I am not talking NTR, as everything that would have happened is set in the past, it's more in a change in characterization from the early game. I think a lot of characters had this happen, but Zoey had it worst of all.
It has to do with a difference in how she was set up early against what she ended up becoming. It has been a long time since I played early Zoe content, but it always felt strange that the early story of the game had Zoe, the best friend of the MC who CLEARLY has a major crush on him since before the game begins, is generally shy around him, and even has shy issues showing him her boobs at all, suddenly in her head and bits of dialog talks about how good she is at giving head, how big the MC was in comparison to others, etc. It has little to do with her being a virgin or not, at least not just that, more on how there seems to be a change in her character and loss of consistency with it, back early towards the end of S1.
If she was head over heels for the MC, and we know he never dated anyone, and we know they were friends forever so there is a disconnect in her character around that point. Could be intentional due to the strange happenings in the game itself, but early Zoey is set up as the more or less virginal childhood friend, and takes a sharp turn.
Which is odd, considering that Ellie the one who is willing to get naked and take it up the butt within hours of meeting the MC, is the actual virgin in the game. I don't know if there was a change in writers at some point during development, and maybe S1 which I have not played since the game was still called Echoes of Lust had dialog changes that make everything sensical now, I am going on memories of the game since the initial release.