you will cough it out on your own, the doctor will treat the cause of the reflux itself by doing tests and most likely putting you on meds to treat the reflux itself.
garret.. if you get bad acid reflux you can actually breathe it into your lungs.. it won't "fill" your lungs by any means, but just a bit of aspiration into your lungs can cause irritation to the lining. For me it results in asthma attacks when my reflux gets really bad.