There really is no way to tell what MICE are thinking or why for sure they do certain things. I will however say this, when I was breeding mice, because they do seem to eat thier babies alot more than rats, I did not change thier bedding immediately, I waited at least a week, but if I HAD to change thier bedding and fuss with them, I would scoop out the WHOLE nest, with old bedding and babies, and place it right into a corner of the clean enclosure. You really want to limit fussing with them as little as possible IMO for the first few weeks. I also noticed, when I was breeding them, sometimes they will tend to do what looks to be singling out certain babies, but if the litter is HUGE, the female may not be able to care for all at once and needs to separate them into smaller groups for thier care. Also, it could actually be that they are singling out certain babies, this is natures way for getting rid of the weak. The fittest survive, and this behavior ensures that. Also, did you know that most likely, your female is actually pregnant again? Rodents can become pregnant almost immediately after giving birth, from my experience, I have seen this to lead to Mom putting out babies to make her litters smaller, cause she knows she must get them weaned and on thier own food intake before her new litter is due to be born. It is best to separate your male and female so immediate pregnancy does not happen so soon after birth.