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.