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I wait until the babies have their eyes open before I clean cages. However, I handle my babies from the time they are 24 hours old. I've only had one experience like you are describing, where the mother buries the babies, but she literally buried them under the bedding. Needless to say, they didn't make it out. I gave her a second chance at being a mommy before I left her go, and she is doing great this time. She raised 10 healthy babies. I have noticed though that a lot of my does do block off the entrance to the babies (they get the castle-type plastic houses). I don't think it would hurt to look at the babies and make sure they are being fed and have little bellies full of milk, especially if ypur does are tame enough and trust you enough to handle them.
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