Dear njam, welcome, you have found the most wonderful site. I too had years of hoarseness, coughing, throat clearing and difficulty breathing. My asthma/allergist did a scope and found LPR, since I was already on Protonix once a day, he upped it to twice a day and for a while it helped. I got worse though, much worse and his partner starting talking about vocal cord dysfunction. In the meantime my breathing difficulties persisted and got worse too; eventually I was sent to National Jewish in Denver; they finally diagnosed vocal cord dysfunction, mixed bronchiolitis and with an incredibly thorough workup by a GI specialist out there, found that my reflux was through the roof. My Johnson-Demeester score was 126 and I had a whole host of reflux induced problems, including a hernia that we also didn't know about. When I came home, my GI and Family Dr. decided to send me to Cleveland Clinic, so last spring we went there and again underwent a ton of tests which confirmed this. In July I had a Nissen and since then I have had no problems at all with the vocal cord dysfunction, hoarseness, coughing, throat clearing.
It was not cancer, nor were there any signs of a precancerous condition, but the fact is that the acid can and will damage your throat and larynx. Please follow your Dr.'s advice, get a good..really good..gastroenterologist and have a work up done, including endoscopy (which is no big deal). Good follow- up-news, my vocal cords, while scarred, are not damaged beyond repair (so to speak), my larynx healed on its own; the lung damage is permanent but since the acid isn't getting into my lungs anymore I'm breathing much better, and my "allergies" are much better too.
Get it checked out, feel better!!