Emily has been able to recover from some mild colds on her own without any intervention, so I'm glad we don't start abx at the very first sign of a cough, but at the first sign of congestion or cough we increase vest and nebs. If this doesn't help and she is still coughing several days later I call her cf center and we decide what we are going to do about it. I call sooner if certain signs are present (shortness of breath, coughing up bloody sputum, big impact on overall qol); wait a little longer if she still has good energy levels and appetite and just doesn't seem that sick compared to her bad exacerbations.
In any case- we don't wait an extremely long time, not as long as I'd wait to call the ped if my boys were sick; it's a very different situation. With her being colonized with staph and the fact that it starts multiplying at the first sign of illness, and with having all that inflammation and thick mucus down there, we can't afford to let too much time pass before starting to treat it.
I would not be as concerned about abx weakening her immune system (I understand your point about the impact they have on beneficial gut flora, but they do not weaken the body's overall immune response) as I would be about infection causing permanent lung damage. Over time, you can figure out a way to get her to take probiotics (they can be mixed into a small quantity of soft food too, easier to ensure they are finished vs. giving in a bottle, or you can give in a small quantity of milk/formula when she is good and hungry and when she finishes it, the rest of what she normally drinks can be added.) My daughter takes a multi-strain probiotic as well, which we increase while she is on abx (fortunately she is old enough to swallow pills.) Upon advice of some other parents here who use them, we give them to her several hours apart from when she takes the abx.
