So sorry!!! Finding dead babies when you think you're out of the danger zone is crushing.
Two things jump to mind as possible explanations.
The first is mice... I've had does absolutely lose their minds when mice got into their cages and/or nest boxes while they had young kits. They usually tore up the nest and stomped every last kit.
I'm assuming it was their attempt to kill the mice, but of course it totally backfired, not that they understood that. I've learned to have a zero-tolerance (or as close as realistically possible) approach to mice when I have pregnant or nursing does in the barn. They also often reject a nest box if it's had mice in it while it was in storage.
The other thought, is that this is the kind of thing I've come to almost expect when I breed (or used to breed) for December or January kindling. I've written about it on other threads, but I have by far the highest incidences of kindling outside the box, not covering litters, scattering litters, not feeding kits, abandoning nests, chewing ears/legs off, and every other malfunction you could list, during those two months. This includes new does, old does, and everyone in between. They don't *always* mess up, but it's dramatically more common than in other months. I don't think it has anything to do with the cold (I've had does do great at well below zero in the spring and fall), but more that their hormones are on winter watch and don't help the doe do what she needs to do.
I certainly wouldn't write her off, but make sure your barn is mouse-clean and give her another try in a month or two. February litters are nice.