I'm new to this so please take that into account when you read this.
It seems to me that treating your whole flock (sick ones and non-sick birds) with an antibiotic is a
big mistake. There are very few antibiotics available to our backyard flocks without a visit to a veterinarian. If you treat them frequently, just as a precaution, it seems that you will get resistance to the drug over time. Then the drug will not work as well or as quickly as the first time you used it if you need it again later. Treat sick chickens only when they show signs of being sick and isolate them for the entire time that they show symptoms...plus a little extra time. It takes time for the body to shed disease through mucus membranes and chickens are great at hiding symptoms from the rest of the flock (they get pecked when they show weakness). I usually isolate for at least a week after all symptoms disappear and I always understand that re-introducing a potential disease carrier could endanger the entire flock. The only other thing I can recommend is that
if you can get a firm diagnosis for what disease you are fighting, then there may be a vaccination available for that particular disease. You can treat the symptoms in the sick ones and vaccinate after all symptoms have gone away. Vaccinate all of your other birds that will come into contact with the re-introduced birds. I believe that your carrier birds will show symptoms again after the vaccinations....not sure that this is correct...maybe someone else can chime in on that. If so, you can cull or isolate that bird indefinitely.
http://edis.ifas.ufl.edu/ps030
Good luck!!!