On my playthrough of Pandora's Box, Eugene and Nadia got married at the end, which means they technically still are, even if they've not seen each other for 19 years. But neither of them act like they're still married, and there's been no mention of a divorce, so I don't know whether they are or not? It was never really netorare anyway, more netorase, because Eugene never seemed overly concerned about Nadia having fun with other guys. If you want Eugene to have any significant sex, you have to make him submissive, so at this point the only NTR is going to be netorase. My Eugene seems incredibly easy going, and just goes along with whatever the women in his life want. And that seems to work for him really well.
So I don't know what will happen, when they eventually meet up. I doubt anything particularly incestuous will happen between Eugene and Ellie. I think once he realises who she is, he'll want to be her father, rather than her lover. And whether that will involve Nadia as well, I don't know? They certainly have unfinished business, but whether they can rekindle their love who knows? And how will he react to Nadia and Ellie, both prostituting themselves?