But she has been staying there on and off with the baby- there is a baby tub in Mulder's bathroom and baby stuff all over the place. She obviously has to have somewhere set up for the baby to sleep.

Oh, I wasn't questioning that. Just that there's no mention of the baby being put down to sleep, or anything along those lines. William is so present in the whole of the story that this sudden absence seems a bit jarring to me.

I don't think that Will(iam) was born when this story was conceived so I don't think that she knew whether or not Scully was breastfeeding.

Oh, I forgot about that. Good point. Even though Scully is a doctor, I somehow can't see her choosing to breastfeed. But as you point out, this is an odd discussion to have here...