Considering the position and assuming the baby is treated as an independent being instead of part of the body... must probably would be digested... lol
It probably goes to the same hammerspace dimension that the uterus goes to. Like, people only think about it when the topic of "what if TS when preg" comes up, but there's a lot going on internally that raises questions even under "normal" conditions. Whole organs are seemingly being created ex nihilo and vanishing just as easily, so where the hell are they coming from/going even when there isn't a fetus involved?
Like that one time Mahiro headpatted Kaede for working hard, and then when asking about what she’s going to do with the work money, Mahiro mentions a bike. That’s 100% an onii-chan move that went natural.