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It is quite common for mums to move litters and also to have multiple nests. Sometimes they even have some pups in one nest and some in another and will tend to both lots separately. Dwarf pups at 3 weeks are quite independent and should be eating well. Supplement with baby food and protein such as tiny chopped boiled egg, plain chicken cooked rice and pasta as well as little bits of veg / fruit and plenty mix. They should do fine. Give them loads of bedding to keep warm too and ensure the males and females are separate at 4 weeks. If there was only one female I would leave her in with mum.