Welcome to the Forum ! Sorry to hear about the “bump in the road,” but it probably isn’t the disaster that you have imagined.
First, a word of caution about urine cytology. It is very helpful as a diagnostic test, BUT ONLY IN CONJUNCTION WITH OTHER TESTS. Unfortunately, urine cytology tests tend to give too many false positives to be used without other methods of diagnosis. That is why your dad’s urologist is doing all the other tests.
The other symptoms you mentioned are likely to be side effects of the BCG treatments.
If the urine cytology results prove to be accurate, the likely reaon would be that the CIS is still present, not that the cancer has metastasized. If this is the case, the urologist has other tools in his tool box to try to deal with it.
Wishing you and your dad all the best
Sara Anne