I would let her continue setting. You said they were at difference stages in development, so that means possibly other hens laid a few eggs while she was sitting. She will take care of the chick and continue to sit on the other eggs until they hatch. I wouldn't worry about the size of the yolk sac at this point. A hen is the best option for raising chicks, so I would not opt to intervene. Hopefully soon you will see peeping chicks.
