She sounds like she's doing a good job. I'd just leave them be and see what happens.
Mother hens don't clean their babies like that. I'd continue treating the one chick until he gets better.
How long has it been since the chicks hatched? Is she taking care of them by showing them where food and water is, calling to them, keeping them warm, etc?
It sounds like she was confused after only sitting for five days and didn't recognize the chicks as her babies, but if she sat her full time and still rejected chicks, she's just be a bad mom. That's how some hens are. Despite being excellent at sitting, they make terrible mothers when given...