Ovarian cysts can sometimes cause abdominal pain, but hormonal imbalance doesn't.
Most likely you have no further ovarian cyst, since the pill tends to prevent ovarian cysts.
It's not possible for me to know what the cause of your abdominal pain is, and you would probably need a careful exam by a good doctor plus possible testing to figure it out.
I would suggest getting a second opinion from another doctor. Best wishes.