They likely have CRD... sneezing and coughing, some listlessness, eye watering and some nasal watering/discharge is common. Look up CRD and/or MG, etc.
MG is especially slow moving through a flock... incubation is 6-21 days. This means it can take awhile to move through the whole flock. Some of them may not have gotten sick immediately in the first go-round, and now they're getting it, or they could be 'relapsing'. It's a CHRONIC...and once they've contracted it, they're carriers forever. They may never get sick again...or they may show symptoms under stress. They will infect new birds, and it can be passed on thru the eggs to the chicks. (eggs/meat are still safe to eat, however)
Your options are:
Treat it-- if/when symptoms reappear. It'd be best to separate the sick birds and treat only those showing symptoms. You cannot 'cure' them, but can manage any secondary infections that may arise during a flare-up. Isolating/treating only sick birds would prevent you from tossing eggs from the entire flock and prevent those NOT needing meds from being subjected to them.
NOT treat it. Within this option are a few options, too. Some people (that aren't culling the entire flock) will NOT treat those with symptoms... if they 'make it' and 'beat it themselves', they feel that's what makes the flock healthier-- weeding out those that can't overcome it/live with it without constant medication. Cull those that obviously aren't doing well on their own... or let 'nature takes it's course', but that kinda seems harsh if a bird is suffering with a severe secondary infection. Or cull any that show respiratory symptoms as they crop up, immediately.
OR-- cull the entire flock, sanitize and wait some time a bit of time for the virus or bacteria (MG is a bacteria, but behaves like a virus, which makes it capable of going into carrier status) If it's MG, it only survives about 3 days outside of the host. SOME of the things birds can carry, though, can live months outside of the host in the right conditions...
IF you cull and start over, don't buy live birds UNLESS they are day olds (preferably from a hatchery that tests for MG/CRD since it can be passed to the chicks via carrier hen in the egg-- but this is at a much lower rate of transfer than direct contact with sick birds) or buy hatching eggs from 'clean' stock. Practice very good bio-security and never bring a live bird onto your property that could be a carrier of MG or any of the other illnesses that leave them as carriers.
It's thought that the % of backyard flocks that are infected (carrier state) with MG or one of the other CRD illnesses is upwards of 80-90%. Many people have no idea... the initial infection may have been passed off as a "cold" (which chickens don't get in the sense that humans do), and then they remain carriers. With MG, the symptoms can be fairly mild...not all show symptoms (but can still be infected) and mortality is usually low in older pullets and adult birds. Not ALL in your flock MAY have it... or remain carriers, either. Without testing, it's impossible to know (or know EXACTLY what it is, too...but MG is likely contender). Some birds seem to resist it... others have more 'flare ups' and don't deal well with it.
The birds that are sick now, do you know if they showed symptoms before? Perhaps they're just picking it up from the others, given the way it tends to move slowly through flocks. If they were definitely infected before, any number of things could make them have symptoms again--- stress (heat, cold, being moved, new birds, change in flock dynamics, etc).
WHATEVER it is... know that it's a carrier disease (most things called "colds" in chickens are) and even if they recover after the initial, acute infection- as it moves thru the flock- and never show symptoms again...they WILL infect new birds. You shouldn't sell hatching eggs, live birds, or show your birds... basically, a live bird should never leave your property. Any friends with birds should be careful, very careful, to not track it home to their flock. Likewise, care should be taken so that you don't track it to 'clean' birds, etc.
Sorry it's not better news--
It's up to you how to proceed... it's a personal choice. Some cull immediately, some 'live with it' and take necessary precautions... and those that live with it, vary in how they deal with any flare ups. (as I said, some choose not to medicate... birds that overcome it and remain healthy get to stay, birds that can't deal with it-- are gone, one way or another. That's another personal choice to make.)
