Kath,
Welcome. !st, none of us are doctors just people that have been there and done that so take it for what it is worth. If I understand correctly Dan has had 2 courses of BCG? With biopsies not showing tumors and a cytology showing malignant cells. I would rely heavier on the biopsies pointing to no cancer. Cytology is notorious for false positives. It even happened to me.
A CT Scan would look at the whole urinary tract to rule out other involvement since he has had prostate cancer. The only downside CT scans do involve a SMALL risk either in the contrast dye or radiation (which has never been proven yea or nay but many questions). This may become more important if cytology keeps showing atypical cells.
On the BCG. He probably has had some good value in it with 2 courses and if the bladder is beat up over this it may be time to discontinue. There is no "exact" protocol done by everyone. My URO did 6 on, 6 weeks off then 6 and that was it. Last item in BCG. Lower dosages have also been chosen at 1/2, 1/4 even 1/10th if side effects are too much and you want to continue.
I have written a book and hope I haven't made this more confusing. I have learned asking questions of your team is the best answer. Last item. There is a good chance that TA "tiny" tumor was eradicated in the original TURB and is gone forever. Keep those 3 month or followups. the scopes are a real key.