Finkie, so sorry you're going through this. It never seems fair when good breeders who care so much for their dogs and puppies have nothing but heartbreak after heartbreak.
How old are the pups now? I would definitely not trust the bitch with them unsupervised, even if things go ok with supervision. Having known people who had issues with bitches attacking their puppies or worse, it seems it's pretty likely to happen again if they are left unsupervised. Often, it happens again in subsequent litters too, although I think there are times it is due to an overly stressful situation. I really hate to say that but...I really think you are better off not leaving her alone with them