People with Lupus can experience amenorrheic (no periods) or oligomenorrheic (scanty periods), or they can bleed very heavily. Often times, the disease can worsen (flare-up) during the menstrual cycle, most probably due to fluctuating hormone levels. Many women feel that their Lupus worsens during menstruation (especially during the end of their cycle). Researchers feel that
estrogen may be the cause of making the condition worse, and this problem is currently being studied. So, what you are experiencing is not uncommon. I could not find information linking Plaquenil with menstrual problems..sorry.
Peace and Blessings