Well most of the latent feelings are going to be there, remember he chose Maya over Niki and it's likely he was with Maya before he actually broke up with Niki.
Not only that but Maya has been the one proper connection for him through all this, and even without his latent feelings from his past (which he partially remembers but are probably still shining through), she's the one he's always gone to to speak about the reset stuff and has been alongside him through this mess.
And as time grew through Chapter 3 and he learnt more about himself, he always returned to Maya, and would drop everything for Maya. Remember he chose just being close with Maya over having sex with Noriko, which is a pretty pivotal moment for this sex-crazed groomer. When he learnt his name? He called Maya.
It's also been shown that Sensei does not deal with loss well at all. After Sekai died he completely broke down (He broke up with Niki and shut almost everyone out, maybe except Maya?). He's still haunted by it, showing he definitely has some of his memories and is just repressing it. Now add that it's Maya into the mix and you've got a perfect recipe for someone breaking.
Because unless I'm recalling incorrectly, Sensei never actually knew what fully happened during Bluejay, he didn't actually know Makoto killed herself but the world reset it.
Hope that explains a bit.
