Welcome to Healing Well! It sounds like you need to stay on the Protonix to keep those symptoms at bay. I suffered from GERD for many years, and was on a number of different PPI's--Prilosec, Nexium, and lastly Protonix 40mg twice a day (I started it after a GERD episode that landed me in the hospital with uncontrolled asthma as a result).
You need to make your own decision about how you handle your GERD problems, but I can tell you that I've been taking PPI's for at least 15 years. Although I still had some breakthrough reflux, and still got GERD related asthma symptoms, the PPI's definitely decreased my symptoms markedly.
I can only speak for myself, but I couldn't have done without them. Fortunately, I've had the Nissen Fundoplication, and have enjoyed being GERD free for the past three months.
I wish you lots of luck with your problems.
There are lots of people here who have experienced problems like yours. I hope you'll continue to post, and I'm sure the many very caring members here will be happy to help you work through this problem.
I hope you feel better soon.