I really don't understand people expecting someone to recognize a person they met a few times over 20 years ago -- if not more (Chloe's 21st birthday has past) -- when they watched that person grow up from a baby. Even if his face tickles her memories, there's no way she would ever think he was the same person unless/until she knows about the time travel.
The real question is ... where was MC during the time travel? The update made it seem like he's supposed to be older than Chloe, but even though the twins should have already been in the picture, there was no indication they even existed in the past.
So maybe there's more of that story to be told. Or maybe the inconsistencies are there to stay.
Also, might want to try downloading the patch again. I only had a couple names where it could have been relationships, and no "roommates" listed.
I would say if I fucked someone and wasn't drunk I'd remember them, 20 days or 20 years after, esp if I was in love with them and they got me pregnant. And I would certainly be wondering wtf the glitch in the matrix was that made them look identical to my current relative, all unlikely shit kept on the table until specifically ruled out (time travel, gov't genetic experiment with my family the random unwitting guinea pigs, visitor from parallel universe, etc). And yeah, stories that involve backwards time travel always tend to get fucked up, probably why it will never actually be a thing in the real world (and even those that only include going back to where the time machine is first turned on but not before is a stretch, even if physics allows that on paper). I'd think the MC can't be in both time periods at once and that does seem to be the case when he disappears rigth in front off his friends/family on a couple of occassions and when he does an extended stay in the past he's no where to be found in the present for the same amount of time, but I'm not sure if that includes all time in between. Like what would happen if he could go back to only 10 years ago and met his 8yo self? or, worse, what would his family think if it was only 1 year apart? Would there be 2 MC's? Only 1 year of difference would be practically twins, as people don't change that much in a single year if they are already late teens in age. As far as Chloe being 21, surely that's a mistake and only mentioned since she was out drinking, which simply mentioning a fake ID would have sufficed (or out bar-hopping in some foreign country on vacation, most countries you can legally drink at 18, the US is just weird in that regard). 20- year fixed gap with past and present comoving + 9 months of gestation, so can't be older than 19y3mo, not 21. Maybe 19y5mo if she was 2 month premature, but that's pushing it. Which paradoxically makes her older than her dad/cousin, since he's still 18 + however much time passed since the start of the story.