Unfortunately, I know this all too well and I will share some of the things that the vet told me and what I learned from the experience of having 4 back to back surprise litters per bunny (8 total):
It is sadly very common for bunnies to lose half or more of their litter, especially when there is an underlying cause, such as the pregnant doe not getting enough good nutrition, being handled wrong when pregnant, being exposed to chemicals or poisons, or something in her or the buck's genes.
My two bunnies lost 50% - 70% of their last two litters due to some being born deceased (many were deformed) and some tragically passed as late as 7 days old, which is pretty devastating. The vet believed it was the lack of a proper diet during pregnancy or being exposed to something poisonous. As someone said, runts do not make it often, but we cannot assume this is almost a guarantee-- four of my runts survived.
Please make sure the babies are warm, are being feed, and strong. The belly should be round and not wrinkled at all unless it is close to feeding time. If a bunny has visible ribs and wrinkled skin compared to the others, please do not be afraid to gently hold them up to her nipple to nurse it, while stimulating down there so he will urinate after
However, please do not be worried if you do not witness the bunnies being nursed-- they often do it once or twice a day-- usually early in the morning, then in the evening.
Also, please avoid putting long pieces of hay in the nest when they are not old enough to nibble on it, because the babies can get poked in the eye and it will be damaged. This happened to my girl, and she has a permanent blue scar over her eye.
Sorry for your loss, losing baby bunnies truly hurts.
