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Hmmm. Since your E2 wasn't that high I wonder if those follicles were just leftover cysts from the previous cycle. As long as they arent too big- greater that 25mm and they aren't producing estrogen they should have an effect on your cycle.
I haven't done EPP so I don't know the specifics, but I think using estrace in the luteal phase is similar in theory. Basically the extra estrogen is supposed to quiet down the ovaries so early follicles aren't recruited. It works better for some than others. Might be worth asking about since you're already taking progesterone. Usually they are prescribed together if estrace is used.