Hello,
Microscopic hematuria can be due to urinary tract (bladder) infection, swelling in the filtering system of the kidneys, stone in bladder or in a kidney, blood disease, like
sickle cell anemia, certain medicines
and tumors in the urinary tract.
You have already undergone cystoscopy which has ruled out most of the cases. I suggest you to get done an ultrasound abdomen to look for any kidney stone and blood tests for sickle cell anemia.
I hope it helps. Take care and regards.