Hudson,
I am 7 years free and I schedule my annual cystoscope 6 months apart from my annual physical, so a cytology can be done every 6 months. In March with my physical my GP's cytology showed a few atypical cells and immediately wanted me to see my URO. So I did. Once I showed up the URO said "what was I doing there" the test was of no concern. Besides a scope possibly tainting your test, my reading indicates an early morning sample can be often faulty so a second or later sample is preferred-mine was an early/first sample. That said, I will be certain to keep my cystoscope and cytology in 2 1/2 months, As far as the FISH. He said dislikes because of too many false positives, so he doesn't do them. Listen to your body (basically self watch your urine and been self diligent for any unusual pain or discomfort or changes). I have to take strong antibiotics after every scope because we stir up beasties.
Net/net, just be sure you keep your 3 month follow up or maybe accelerate it by 2 or 3 weeks if you have more concern.