The endoscopy is nothing to worry about. You don't remember anything from the procedure...the only side effect is a sore throat for a few days. My view is that the test is the only definitive way to tell what's going on. In fact, doctors shouldn't prescribe Nexium until they do the endoscopy! It's true that they can find acid reflux, but they can also find clues to many other conditions...
In my particular case, I was diagnosed with "acid reflux" from the Upper GI Series. The prescription was Nexium...at first I felt ok, and then with time, I started feeling worse and worse. I was convinced that the Nexium was exacerbating my symptoms. In any case, the endoscopy showed bile to be the cause, not acid. If bile is the problem, PPI's will actually do DAMAGE to your system. The reason for this is that the stomach produces hydrochloric acid to counteract the alkaline bile...then if you were take Nexium, imagine the pain!
So I would say definitely do the test. At the very least, you'll feel better finding out what's wrong with you.