Ovarian cyst

So on September 1 I went to the doctor for excruciating stomachs pain to find out I have a cyst in my left ovary. They found it when they got back the results of a CAT scan and they wanted to see the results from a ultrasound. They did both transvaginal and the pelvic ultrasound imaging. The doctor couldn’t find the cyst when she performed the transvaginal ultrasound (which she did first) and neither on the pelvic imaging ultrasound. But they said that I had it and to wait it out and it should be gone within a week. When I went to bed and woke up the next morning I saw that my period has started (after being a month late) does this mean that the cyst is gone? Because I don’t have side pains anymore but now I am in my second day of my period and I’m still feeling cramps and back pain. Usually it only lasts the first day. And they won’t go away with any pain medicine.