Thanks for your question. The scenario you describe are probably two unrelated issues. Skipping your menstrual cycle without evidence of pregnancy usually indicated that you had a menstrual cycle during which you did not ovulate. A cyst may remain on the ovary while this resolves and these types of cysts can cause discomfort. When ovulation does not occur, the ovary continues to produce estrogen with no progesterone to balance out the effects of estrogen from the follicle (egg) cyst on the ovary. This may delay menstrual periods, cause breast tenderness, and produce cramping or pain in the pelvis. These cysts usually (97%) resolve on their own and menstrual periods revert to normal in 1-2 cycles. The cramping you are experiencing may indicate you are about to have your period. A pap smear showing a shift in vaginal flora may indicate that you have a bacterial overgrowth. There are bacteria in the vagina that fight off infection, but if infectious bacteria overgrow, these protective bacteria may be overpowered and an infection known as bacterial vaginosis may occur. Watch for symptoms of increased discharge, odor, irritation and discolored discharge which may signify the onset of bacterial vaginosis. Treatments are available for these infections from your gynecologist. I hope this answers your questions. I am available for further consultation if needed.