Wow....can see why you might have some questions! Please remember that we are not doctors here and are not competent to give medical advice. So anything I say is sort of off the top of my head.
First, FISH tests are a very useful help in diagnosing bladder cancer, but do have some issues. One of these is that they often present false positives...meaning that they may indicate the presence of cancer when there isn't any.
Second, a cystoscopy is not a final test for the presence of bladder cancer. It is a very important first step and usually the urologist can see what look to be tumors but not always. There are some forms of bladder cancer that do not present as discrete tumors, It is necessary for him to do a TURB where the tumors are actually removed and sent for pathology before cancer can be diagnosed for sure. Third, there are many reasons for blood in the urine that are NOT bladder cancer.
Because of the uncertainties, your history of smoking (are you quitting?), and the slight ...although remote....genetic connection, you might feel better if you had a second opinion/consult.
Sara Anne