Acid reflux/gerd/barretts esophagus are common with lupus as are other GI issues. If you have not seen a GI doctor you should. I have had one for 10 years and he is a valuable member of my medical team because I had all sorts of GI issues including barretts. I also have polymyositis and acid reflux problems are more common with it than lupus.
A GI doc might want to do an endoscopy or colonoscopy to accurately diagnose what you have and how to treat it. Neither is a big deal (except the prep) and are usually done at the same time.
Diet and proton pump inhibitors can keep you well but lupus itself has to be controlled.
MCTD (SLE Lupus, polymyositis, scleroderma). Diagnosed 2005. Kidney, liver, GI tract, dysphagia, raynauds, barretts esophagus, quadriplegic in 2005. Recovered and now active in downhill skiing, golf, hiking. Meds: amlodipine, benezapril, omeprazole, potassium, folic acid, vitamins, maxide.
Remain Optimistic and you can overcome.