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Progestin only BC stopped period but they're back again randomly, why?

My girlfriend has been on a progestin-only BC since July, she tried normal estrogin based ones as well but they do not work well since she has ovarian cysts. She didn't have a period for 3 months but they randomly started again. She is taking BC because her ovarian cysts make her have very violent periods and she wanted them to stop but they're back again. Why are they back? Her doctor wants her to try the shot but she already had nasty side effects when starting the pill, if she gets side effects with the shot it will last much longer. I just don't want to see her in pain anymore, it almost hurts me more to see her suffer. Any advice is appreciated
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973741 tn?1342342773
How are things going now? It has been a while.  Manipulating with hormones is always a fine balance and changes that occur synthetically from pills or shots can happen as well as our own body shifting things.  If she has ovarian cysts, she likely was passing a cyst or had one at that time.  This is not dangerous but uncomfortable.  How is she now since some time has passed?
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