Now is certainly not the time to worry about breeding her again as you just need to let HER and YOU deal with the loss. She will likely grieve as well. I 2nd the fact that it is more common in large/giant breeds for things like this to happen, just odd w/only 2 pups. It *could* have been something wrong with him. How old was he? We had a scottie when I was a kid who intentionally killed all but 1 pup out of each litter (we saved the 1 each) and each one of those pups had horrible health issues...so it very well could have been that, but in all likelyhood, it was just a pure accident, and there is no one to blame for it. Just be happy you still have a healthy Abbey (the girl you have loved for a long time.)
Kristi