Cyst gone, appendix out?

Yesterday we went to the doctor and it was very shocking! My appointment was at 10am and we didn't leave until noon. I actually saw 2 doctors. The first one did an exam and was going to send me home to wait and see. They said to call if I got worse. We then explained that I was already worse. I have been to the ER twice and I'm on so much pain medicine. I told her that I could go to the ER everyday because it hurts so much. They finally understood how much pain I'm in. I actually saw a nurse, not the main doctor first. Apparently it takes months to get into the doctor. Once the nurse understood how much pain I'm in, she went to get the main doctor and he wanted to see me immediately. He came in and asked if we had had my appendix checked. We said yes just by blood work. He pressed on my stomach and I about died. Once he did that, his whole demeanor changed. He didn't talk about my cyst anymore. He said in the past 3 weeks, he has seen several women who come in with what they think is cyst pain, and it turns out to be their appendix. He said that he really thinks that's what's going on with me. We talked some more and he wanted blood work and an ultrasound. The blood work is to check my appendix, the ultrasound is to see about my cyst.
I had the blood work before we left his office. My ultrasound was scheduled for yesterday at 3. The ultrasound technician said that my cyst is gone...that's right GONE. So that is not what is causing the pain. That makes it more likely to be my appendix. We were shocked. We thought my appendix was ruled out. The doctor said that we should get the blood work back soon and if it is my appendix (which he's pretty sure about), then he would remove it as soon as possible. You don't want to mess around with that.
So, why did the ER say my appendix was fine? He explained that they just look for infection. The extensive panel that he did, shows more like inflammation and things in detail. It would still need to be removed asap.
It would make sense that it's my appendix because I just haven't been feeling well since the pain started, and a cyst usually would just cause pain. We thought it was weird that the doctor never went back to the cyst, he was focused on my appendix. He's pretty sure that's what it is.
I have an appointment with the doctor again on Wednesday. If I get worse, I will go in sooner. Until then, I can't be alone incase it were to rupture, which most likely is not going to happen but we have to be careful.
It was a crazy day yesterday with many unexpected things! I'm just ready to get whatever it is taken care of.