@mish239 from my experience they allowed the cycle to continue but only were able to take the follicles which they could access on the left side. My cyst (5cm! Of yuk) it was so big it blocked the right ovary. In theory follicle cysts are suppose to go naturally and disappear over a period which is why you probably they want observe if it's shrunk but they also might want to monitor that it's not getting bigger too along with the rest of the follicles because of the stims.
Try not to worry to much yet, you might only have a small one which is on it's way out. Follicle cysts are really common and most women have them and don't even know.