I actually use cleaning time as a good time to check out the babies without momma rat hovering over them and getting in my way. Just pop her into a secure container, pop out the babies and have a good look over them for growth, milkbands (if visible) and general health. Clean the cage, scoop out a slight depression in the corner momma rat prefers and pop the babies back in there. Add in momma rat and she'll happily do the rest. I've never had a female rat reject her young because of cleaning or my scent on them. She may for a moment ignore them as she checks out her clean digs and grabs a drink and something from the food bowl but she'll soon go back to the little leeches that are hollering for her.