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Lots of mice hide the entrance to their nest, it's an instinct to protect them from predators and even the weather. It doesn't sound like they've been abandoned. If you are desperate to look and can do so without disturbing the nest/bedding then remove the does to a spare cage where they can't see what you're doing and take a brief look. Don't keep the does away for more than a few minutes though, since it's the first time you've done this and all you're doing is checking the babies are being fed. I wouldn't clean the cage at this point since your does are not used to you disturbing them.
 
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