It is reasonable to repeat the ultrasound after the menstrual cycle.
If you have a history of endometriosis, it is common to continue to have findings of endometriosis such as endometriotic cysts.
A CA 125 may return elevated if the cyst is from an endometrioma. However, it might be good to get a baseline.
There is nothing about your history so far that suggests that a gyn oncologist would say anything different - unless you having a growing or persistent ovarian cyst after another ultrasound.
You can lose your ovary with surgery. However, if you have a persistent cyst after your next ultrasound, a laparoscopy is reasonable
In response to your question about the CA125, my grandmother was just recently diagnosed with Ovarian Cancer over a year ago and she underwent the CA125 test as well. Oddly enough, the test came back normal. After speaking with several doctors on this matter (I am currently dealing with ovarian problems as well), every single doctor i have spoken to has said that CA125's are good as a marker but can often times come up showing a false-positive, leaving many families worried of an elevated count when really, there isn't one. My specialists also told me, apparently a lot of times, CA125's will come back positive if a cyst is present on the ovaries or if the patient is experiencing a flare up of endometriosis.
p.s. in regards to the removal of your ovary, i know that is the last thing you will ever want to do. I am going in for surgery in 4 weeks to get a possibly malignant cyst removed as well as my right ovary and i stress to you, please, if you do not have to get it removed, don't. Please try every option there is possible before going down that road. I am 18 years old and have gone through 2 years of absolute hell, i wish i could be as lucky to save my ovary.
I hope that helps!