A MRI is much better than an ultrasound at showing the tissue. Did you have the sonogram first and then the MRI? What was the time frame between the tests? The ordering of the tests and the time frame between them can make a difference on the likely interpretation. If they were done around the same time, the MRI is the more reliable result. If it visualized your left ovary, then you don't need to be concerned about the sonogram finding. It is common for ultrasounds to have interference and sometimes an ovary can't be visualized. Of course, sometimes a mass is covering they ovary which is the reason it does not show.
Did the radiologist or your doctor refer you to a gynecologist?
I can only speak from my experience and the experience that my daughter had in August. A simple cyst is cyst that does not have separate sections and is primarily fluid filled. Usually these cysts are benign and may go away on their own after a period or two. The size you are describing is moderate and from what I understand doctors often prefer to watch cysts that are under 5 cm and simple to see if they will go away on their own. I also know that sometimes one test will come back stating that it looks like a complex cyst (which is a cyst that does have separate compartments and perhaps tissue as well as fluid) and then another test will come back saying that it is a simple cyst. I don't know why they couldn't see your left ovary, unless something was covering it. Hopefully you will be referred to a gynecologist who will be able to make a plan for treatment based on your specific case. If they didn't refer you already for follow up, I would definitely recommend calling and getting an appointment with a good gynecologist as soon as possible.