I meant about the fact that you're the father or not in case incest was not a problem. If you creampied a girl in the past you would be the father but if you chose not to then the father is someone else. That wouldn't require too many changes imo, mainly dialogues.
I mean, it's certainly doable, but let's think of it this way.
Putting aside the timeline problems someone else pointed out above(most of the girls being either too young or too old to be conceived in 1999, which is generally fixable with just some minor continuity tweaks), there's a couple potential roadblocks here. First and foremost, the reveals. Obviously, if you want it to actually be prominent and noticeable, there has to be dialogue in game that states(or at least strongly hints) that all these girls were born about 9 months after one of your visits to 1999. Where do you fit each of those scenes in? How do you make that topic come up naturally? And, most importantly, how do you do it within scenes that already exist within the game? If it's Jestur writing the scenes in then he can kind of make whatever renders he needs to do it, but if we're assuming this for a patch or mod then it would be pretty difficult to create new renders in the same style for this, so we'd need to find existing spots to fit it in.
Second, we have no idea whether any of the girls'
actual fathers are going to show up in the game at some point. They haven't so far, and they likely won't, but any of them doing so could put the plan in jeopardy. Or at the very least, force you to write around it with a "he's just my stepdad, my real dad left before I was born" type deal or whatever. Already kind of awkward to shoehorn in.
Finally, assuming neither of those becomes an issue(reveal scenes added no problem, no dads in the mix)... does it change anything going forward? Obviously some little bits of dialogue here and there might change, whether just the MC's thoughts or if he tells anybody. But presumably people playing specifically for the incest would want it acknowledged in game. How do the girls react when they find out? It seems unreasonable to assume that all of them would go "oh this boy in my class/that I'm friends with is actually my time traveling dad, neat" and then just kinda keep doing whatever they were doing. Even if they're eventually okay with it, they probably experience some amount of shock and need to digest the information. When will appropriate renders appear for each girl? Will that fit into the game's narrative moving forward? We simply can't say, because we don't know what future scenes will look like.
All of this is to say that it is certainly
possible to just edit a few lines and numbers, make it lightly hinted so that the person playing knows what's up, and let the rest of the game flow, but if you really want the game to acknowledge the fantasy then there are some pressing logistical concerns that, at the very least, probably make it easier to wait until the game is closer to finished to toy around with.