Yes, antibiotics taken for duration can cause your normal flora to become disrupted. The good bacteria in our body, that helps us break down the bad bacteria in our body is supressed when taking antibiotics....and may actually lower your immune system defense. Antibiotics should be taken at the same time as directed.
GERD (gastroesophageal reflux disease) may be indicative of repeated antibiotic use. There are natural enzymes in our saliva and more, different enzymes in our esophagus and more in our stomach and so on. When we take a pill for something our body should do but doesn't do, its off sets our body.
You might want to invest in alergy injections, air purifiers, organic clean clothing, non-scented soaps/detergents and so on. Look for the natural cure or even something other than western medicine. Try chinese medicine herbs from a certified chinese doctor. Sorry I could't help more.