First of all, most of the time it is genetic unfortunately. My sister's Yorkie whom she decided to breed to "get some extra money" has always been aggressive towards other females. She only had the one litter, and I ended up keeping one of the girls and she is my spayed baby, but along with a few health issues she is also very aggressive just like her mother. Thank goodness my sister's dog is spayed, that one litter was enough to convince her. However, I still CANNOT have her around my dogs...given the chance she will kill one of my girls, even spayed. Her daughter is only 3 lbs and isn't AS bad as her mother. She can get aggressive but I can control her because I trained her very well as a pup. If I clap my hands and say NO she will stop what she's doing immediately no matter what. If I hadn't trained her that way, I would not have been able to keep her. My sister's dog is otherwise a sweetheart and is WONDERFUL with people, snuggly and cuddly and a kissing queen, but she just can't be around certain female dogs. Now, someone mentioned about mother and daughter and family ties...that is so true. My sister's dog would NEVER hurt her baby. I can take Dede to her house and they play and kiss each other, wash each other, etc. She KNOWS that's her baby and has never had a single bit of aggression towards her. Also my other spayed girl Maddie has been around for awhile and was my sister's baby's best friend when she was growing up. She wouldn't hurt her either. It's certain females, but you just can't trust them if they're like that, sadly.
I have heard several people say their intact males fight. Mine don't at all. There can be a girl in heat right in their faces and they just look at each other like, "who gets her mom?"
They play with each other, sleep with each other, etc. I trust my boys fully.
My girls are good for the most part, I have had a few aggressive girls and once they showed it, they were petted out and spayed. I have a wonderful little group now...they all get along very well except for the occasional snap over a treat or toy.
Now on the babies, I would never let my other dogs around a litter of pups until the pups are at least 8-9 weeks old, and even then it is extremely supervised. Mothers are protective of their young, it's just instinct, so I would never put them in a situation like that where they felt they had to fight to protect them. Puppies have their own nursery room, a separate bedroom, and I have the door closed at all times and even have the mom inside a big crate or tupperware bin with a hole cut out, covered with a blanket, and inside a big exercise pen. The babies are inside the crate/bin and the mom can go in and out into the exercise area as she pleases, but she always feels her babies are safe and protected. I am the only one who goes into that room, I do not want the moms stressed or upset.
It doesn't sound like you can do much as far as separating, so I would say in that case the only option is rehoming. I don't think you can risk losing either of your dogs OR anymore puppies.