[BonamassaGirl]

My father in Law breeds German Shepherds, and he has one female that he bred once when she was younger, and she killed all of her pups but one, my father in law saved that one, but I remember being so shocked to hear about it, the mom was always the sweetest dog. We all thought maybe it was because it was her first litter and she got nervous, or whatever, but he said that sometimes dogs will do that instinctively if there is someting wrong with the pups, even something that we humans cannot detect yet...

He tried breeding her once more I think a year later, and she killed all of the pups in that litter as well. He never bred her again. She was also the kind of mom that didn't want to be left with her pups, and left them alone often. It was when my father in law penned them up together and away from the other dogs to encourage her to take care of the pups/nurse them, that this happened.

I am so sorry for your loss, I think it is entirely possible what the vet said, that the mom may have been the one to kill the pups, not the other female. But if you didn't see it, then I would look in the stools (like YorkieRose suggested). Not pleasant, but you may get your answer that way-
again, so sorry...