Could Atypical Cells Be Caused By Cystitis?

My name is Brenda, 5'7" 180 lbs. I was diagnosed in 2004. Presented with only the left ear affected. Blood Work sent to Mayo Clinic, confirmed Anti Collagen II. In 2006 had some nasal issues from RP nothing since. I have had microscopic hematuria since 1999 ranging from 2+ to 6+, about 20 different urinalysis and never an infection. Occasionally protein 5+. Had a urine cytology in 2006, negative for malignant cells, had a cytology in Feb 2010, negative for malignant cells. Had cytology 3 weeks ago, atypical urothelial. Have had symptoms similar to Interstial Cystitis for 5 to 6 years. Seems to flare at different times. Good for months at a time. Currently in some type of flair. Urinating 15-20 times a day, lots of burning but urinalysis done on Monday just came. back with blood 3+, no infection. Had cystoscope in 2008 looked good no lesions but bladder was slightly inflamed. I have another cystoscope scheduled for July 18th. I am extremely nervous about the Atypical Urothelial cells but have some comfort that I am still here with hematuria for 12 years. Do you think the Atypical Cells could be caused by what appear to be symptoms of Interstial Cystitis, or do you think it is likely I have bladder cancer. I am going insane waiting. Only one urologist is our town of 20,000.00