Even though the interpretation of Ross losing custody make a lot of sense I would like to point of few things.
Friends has always had a new issues in almost every episode which it attends to so the main focus goes there unless it's about someone crushing on someone within the group otherwise there's a new issue. Keeping that in mind and also how one can see how the show mainly attends to Ross and Rachels love story as the show begins and ends with it, it's seen quite often that while something related to Ross and Rachel being together happens the show doesn't really focus much on other issues on the contrary if something happens relating to the other members ,various number of events take place together.
Therefore what I think is that once Ross and Rachel had the baby the show suddenly started shifting towards Ross and Rachel getting back together or simply their stories in course of that the parts where Ross lives a normal life is covered up by Pheobe's marriage or Chan and Mon shifting or having a baby or anything of those sorts.
Attention wasn't paid to Ross's daily life anymore because storylines that had greater importance were to be attended to.