Yeah, this has happened to me more than once. They do not show up in the adoption pool--they're even gone from any family trees, lke they never existed :-/ I play rotationally, so it's a real risk. In the basic game, pets and children just disappear, whether their adults die or their taken away or, in the case of pets, put up for adoption. I really wish this was different. MCCC helps a little, at least then they don't vanish. But I wish we could sometimes put kids and babies up for adoption like we can do pets, and then they show up in the adoption pool. There's so many cool stories to be done with that! Sadly, I don't think they can account for a birth parent/adopted parent duel situation, which is a shame.
Anyway, yeah, only advice I have is to use MCCC. Then you can go into manage households and decide what to do with your new orphan.