Cysts are ( Poly Cystic Ovarian Disease
) caused by hormone changes . Using birth control pills can sometimes help regulate hormone levels so that the cysts can be taken care of. Your Gynae doctor will likely want you to come back after you have been on the hormonal
pills to see , if the cyst is gone.
At that time the doctor may suggest you stop using the medication or if indicated , you may need to continue it for a bit longer.
Once you stop these hormonal pills as long as there are no medical concerns, you shouldn't have any problems with future in conception ( your doubt wrong )
Mind one thing that many women uses birth control pills ( hormonal pills ) for the purposes other than preventing pregnancy
. Then they stop taking when they want to conceive.
So hormonal pills may help regular menstrual cycle , because they are irregular in your case , may be due to hormonal imbalance.
Hope this information will be helpful for you.