So sorry to hear of your losses, it's always heartbreaking, no matter how many years you've been doing this. A few questions--can you describe the condition of the dead kits? Were they flattened, like they had been stomped on? Chewed on? Out of the nestbox and chilled? Looking thin and wrinkly? Does mama look like her nipples have been used?
Flattened kits in the nestbox often means that there were predators either in or near the pen. Rats can go through a hole the size of a quarter, so the usual 1" x 2" sidewall and roof wire is no barrier at all. Raccoon and other predators can be outside the cage stalking, making the doe anxious. She will often bravely go into the nestbox to protect her young, emphatically stomping her foot to ward off the intruder(s). Sadly, all that stomping often kills the kits.
Rats can chew on the kits from inside the pen, while raccoon and barn cats usually try to fish kits out from the bottom or sides. On another note, rabbits are able to survive amazingly low temperatures safely snuggled in a warm nest of rabbit hair. But, if the doe has peed on the babies, they can quickly chill. Same if she doesn't pull enough wool to keep them warm, or they end up outside the protective nestbox. Does that spend all their time in the nestbox are usually the worst offenders for losing litters, oddly enough. A good doe only goes into the box a few times a day, leaving the babies to snuggle in safely.
If the kits weren't being fed, they will look wrinkly and thin. Well fed babies have very rounded tummies. Nursing does have usually pulled much of the hair out around the nipples, so the babies can be warm in the nestbox as well as nurse easier. Is mama eating and drinking? If mama is off feed, she may not have any milk to give the babies. Is she peeing normally, or is it dark brown (or none at all), which is a sign of dehydration.
