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Are the babies still with the mother? If not, you will need to raise them in a brooder until they are feathered fully, since the mother will probably not accept them. Then is would be best to slowly introduce them to the soil and perhaps give them a preventative treatment of amprollium, coxoid, or whatever medicine you used. I would not combine them into the flock until they are similar in size, but keep them fenced next to the flock.
I would be doubtful that they will stay with the broody or that she will accept them at that age. But since you know her better, you can try with a lot of observation. If the chicks don't stay with her they may be attacked by the other chickens. Have those 2 chicks been given a preventative treatment of coxoid?
Coccidia is not a virus it is a protozoa.
As enola said coccidia is not a virus it's a protozoa and for all intents and purposes it never goes away and is always there...
What happens is that the birds build an immunity to it and are able to fend off it's effects, but it's still in their bodies and around the coop indefinitely for practical purposes...
Medicated chick feed will allow the birds time to build up an immunity...
If you have had an outbreak I highly recommend you get some soluble amprolium and have it on hand (actually all chicken keepers should have some on hand) as the medicated feed is not concentrated enough to fend off an outbreak...