Are the runts really that small? A litter of 10 is pretty much normal and mom has 12 nipples.

You could try taking out the older babies during the day and return them during the night. At 3 weeks they are probably nibbling at the food so they should be fine for 8 hours or so.

Mama will be happy to see her babies so I don't think returning them 24 hours later will make a difference at all. I agree with Some00d, rats are great with babies.