Try putting them on antibiotics like water soluble Tetracycline (check your local feed store, there are different kinds), it may be a bacterial infection or it could be a virus. In the case of a virus, the antibiotics wont help, just prevent a secondary infection. If its a virus, all you can do is just let it run its course.
What you could also try doing is going holistic; maybe some green tea to help immunities and get some electrolytes. Give to them the foods that you would take if you were sick to help boost immunities like blueberries, raw spinach, oranges, cabbage (ALWAYS helps my peacocks!) or some thing like that. You could also try apple cider vinegar, which seems to help just about anything. My birds have that now, and I am trying to get my hands on Oxine, which is supposed to help with the respiratory infections. Many swear by it. Mine are on green tea (yes, I brewed 2 huge pots of green tea!) electrolytes, and I gave them an antibiotic shot yesterday because I could get the water soluble in time...all. 50. of. them. I am getting cabbage and I think I am going to add in ACV if they dont seem to be making a marked improvement.
Dont let the babies come in contact with the ones outside, which if theyre 3 weeks may be difficult, but keep them on the opposite side of the yard or something if you need to move them out. Use sanitary precautions to prevent spreading, i.e. separate feeding buckets, sanitize cloathing and shoes after you care for the sick ones, wash hands, feed the healthy ones first, sanitize the coop and feed/water cups and let them bake in the sun afterwards for a while....etc.
Try and quarentine the ones that are visibly ill, but other than that, there's really not too much you can but prevent the others from catching it. You are ahead of the game with the ones inside as long as they have had no contact with the sick ones.
I wish you the best of luck!
Oh! by the way, I wouldnt kill any of them unless they are REALLY suffering, because a lot of the times if it is a virus, they can pull through. If they make it, their resistance will be much better. Just give them the chance to pull through it...you'd be surprised at what a chicken can handle!
