Can I clean my hamsters cage with babies in?

It is really bad because i was gonna clean out her cage the day she had babies, it was a suprise litter becuase i only had her for a week! they were born on monday or tuesday last week ( i think it was monday) so the cage hasnt been cleaned for 2 weeks. It smells quite bad and their is condensation inside the nest. Can i cut off the bad bedding and add some fresh bedding to the nest and clean the lid while theyre inside? And take the nest box out and clean the wood chippings as well?