The ovaries are located to the side of the uterus and at age 42, are smaller than the tip of your thumb. If you have had endometriosis, that could have eroded some of the ovary making it smaller, and the removal of a cyst could have also removed part of the normal tissue, which could make it smaller still.
The ultrasound sees tissue by comparing the amount of water in the tissue to nearby organs. The more cystic or fluid containing something is, the more it shows up on ultrasound because the sound wave goes through the liquid and bounces back from the surrounding tissue giving it a variable shade of grey, depending on how dense that tissue is.
It is likely that your ovaries cannot be seen both because they are small and because they are attached by scar tissue to a nearby organ such as the intestines. (especially since you have also had diverticulitis).
To help diagnose the source of your pain, you can discuss with your doctor the possibility of getting an MRI to find the ovaries and see if they seem normal. You can also discuss a barium enema to see if it looks like endometriosis is on the intestines and contributing to your pain. That might not be seen by colonoscopy since the endometriosis is on the outside of the intestine, not the inside. Your doctor might also want to do a laparoscopy if the pain continues, though it might be difficult to find your ovaries even then due to scarring. The fact that the ovaries cannot be seen is in some ways good - it implies there isn't a cyst on the ovary which likely could be seen. If you have an ultrasound done at the time of ovulation (get a home kit and follow) the follicle cyst of ovulation might make it easier to find.
Machelle M. Seibel, MD
they always had trouble finding mine and it just so happened that I had kissing ovaries. They were stuck behind my uterus and attached to my bowel. I was diagnosed with stage IV endo