was it her first litter?
I used to breed Dutch Rabbits, until i had to have my whole breeding stock PTS after a diseased male passed it on to all 4 of my females, and my other male.
I used to find this happened a lot with first time mums, killing off their young at such late stages, i think it's the fact that the kits are no longer so dependant on Mum, and she begins seeing them as a threat, and she begins to feel intimidated and scared by them. and she reacts to protect herself.
If not, the kits may have had health problems that she knew were there, and you didn't, or she could just be a poor mother.
I wouldn't feel to disheartened, at least you still have mum, good luck with the next try