Hi Don,
Cytology can be repeated, and needs to be done before any cystos as this can mess up results. There are also different 'grades' of cells that come back with the results, and cytology can show it if it very aggressive, or mildly aggressive.
Guidelines for cytology are sorely lacking and it's common for mistakes to be made as the urine is sent out to an outside lab, and the test is also subjective like pathology is.
The same might go for FISH, that is shouldn't be done too near a cytoscopy which might give false positives= I'm not 100% sure about this though. I can find out for you if you need. It is looking at genetic abnormalites, so maybe it is not affected by inflammation...good chance.
For the record, here is the closest thing to guidelines about cytology tests that we have as of now, I received them from the author in the UK:
Urine for cytology should be the second morning voiding collected directly into a clean container. Approx 20ml is suggested as an optimum volume although smaller volumes are also acceptable for processing by the lab. Samples collected on 3 separate days may increase the chance of detecting abnormal cells.
A fixative may be used if delay in transport is expected, say over a weekend, and refrigeration at 4 degree C is not available. Collection into special fixative may be necessary for UroVysion testing.
Guidelines on urine cytology are being published by the British Society for Clinical Cytology (BSCC) and may become available in a few months. I am not aware of any other existing guidelines on this subject.