I'm dealing with the same thing. I'm fostering some rescue chins and it's going to be VERY hard tomorrow when the one kit turns 8 weeks old and I have to remove him from his mom. I'd kept he, his mom and dad together (ensuring no breed back the first 10 days after she gave birth) and they're a very close family and snuggle together a lot. I am going to put him in a separate cage with his dad. I'm worried the mom will be depressed losing her male partner and her baby boy at the same time. It's not going to be easy. The baby is especially bonded to his mom. (He was her only baby).
The other female I rescued just had two kits (one girl and one boy) last Monday. I removed the father to a cage nearby and he's sulking and barking at me and knocking over his food dish. He's very unhappy not being with his family.
The rescues told me to keep them apart for 10 days so I will and I will only them allow him back with her and the kits if he is gentle with them and there are no problems. Otherwise maybe I can get him to bond with another male rescue chin.
Sorry to ramble....this baby thing is new to me (my own 5 pet chins I do not have in mixed groups and don't have to worry about pregnancies).