Sorry, I do not know where I saw it, but I was watching a webinar of a few urologists. One urologist said that he orders cytology every time he does cystoscopy. He said also that if cytology is negative 97-98% of the time cystoscopy is negative. The problem is when cytology is positive and cystoscopy is negative, then he has to find out the reason. So, what your urologist is doing sounds the right thing to do. Your urologist is trying to find out the source of suspicious cells found in your urine. There can be many reasons. For example, it can come from a tumor in one of the ureters or some other place.
A case in point, a person I know had gone recently to the ER because of pain in the pelvic area. CT scan found a tumor was blocking a ureter and urine backed up to a kidney. He has been middle of treatment for non-muscle invasive, so he must have had several cystoscopies. So, cystoscopy alone can miss a tumor in the ureters.
It can be nothing, but it is good to know that your urologist is taking the extra steps to assure that there isn't anything.
Joe