Hi there, I have been following your posts because my husband had a FISH test due to them finding a few atypical cells on his last urine cytology that accompanied his cysto on his yearly bladder cancer check up. His FISH came back negative, but I have done reading on the test and was prepared for him to have to do exactly what you had done had it come back positive.
That being said, as others have commented, the FISH test is known to have false positives. After all your biopsies and physical looking with scopes plus the CT scan being negative, I think you can be 99% certain the docs are not missing anything. Nothing (and I do mean nothing) in medicine is 100%, so, I would try to not waste much time worrying about the "what ifs". You got great news. Do your best to not dwell on it and enjoy your clean bill of urological health