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It could be hormonal, but bitch-bitch aggression is no joke. Getting one or both fixed may improve things, but be very, very careful when you reintroduce them (likely after the puppies are weaned or even gone altogether). There's a saying that male dogs fight for breeding rights, but females fight for breathing rights. What this means is that when two bitches take a dislike to each other, it can be extremely difficult to fix.

You're doing the right thing by separating now. In addition to preventing injury, maternal stress does impact developing embryos, leaving them to have naturally high levels of stress hormones and to be more anxious and reactive adult dogs. I'd keep the shepherd away from the puppies once they're born, too, since a fight could easily kill a young pup, and it's not unheard of for a female to kill another bitch's pups deliberately either.

If you do hope to reintroduce them once both of them are at a stage where they're less hormonal and stressed (and pregnancy is very stressful!) I highly recommend finding a professional who can help you in-person or (due to the pandemic) via video streaming. You can find someone with excellent credentials for working with behavior problems through IAABC.org or CCPDT.org, both of which only list trainers and behaviorists that pass their rigorous standards for education and experience.

What you can do right now is start muzzle-training, so when you do re-introduce them, you can minimize the risk of serious injury. The Muzzle Up! Project (The Muzzle Up! Project | Muzzle advocacy, Education, and Training) has excellent advice on how to do this. The goal is that the dogs will find wearing a muzzle comfortable and not stressful or scary, so it doesn't contribute to their anxiety or aggression when you have to have them in stressful or triggering situations.
 
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