Pain is always difficult to understand, both for patients and for doctors. What would seem to very painful is often not for some patients and what would seem to be not painful can often be excruciating. That said, since you have had a thorough evaluation of your intestinal tract and now have cysts on your ovaries, there is a good chance (not certainty) that the ovaries are part of the pain, especially since the pain coincides with your menstrual bleeding.
Many women do have their ovaries at age 50, but since menopause is near and your ovaries have cysts implying there might be a problem, it is a time when the decision to remove them often occurs. Recovery from taking out the ovaries by laparoscopy can be anywhere from a few days to a few weeks. Since you are still having periods, your loss of your ovaries will likely lead to some symptoms of menopause and you and your doctor should discuss that ahead of time and decide what kind of treatment you would want to try. You always have a choice about surgery. If you are confident in your doctor and he has explained to you why he wants to remove the ovaries and you have had evaluation for other things, it seems like a reasonable decision to make based on the information you have provided.
Machelle M. Seibel, MD