How can one make up missed prayers whose number is unknown due to performing ablution while having nullifying discharges or being uncertain about the end of the menstrual period? Is it sufficient to perform Sunnah and supererogatory prayers in their stead, or must they be estimated and made up? If making them up is obligatory, must each missed prayer be made up with a corresponding present prayer, and must the making up be continuous?

Vaginal discharge invalidates ablution. You are not required to make up the prayers you missed due to your doubt about purity, because the default state is the continuation of menstruation. The prayers you performed while these secretions were exiting are not valid due to lack of purity, and according to the majority of scholars, they must be made up. However, Sheikh al-Islam Ibn Taymiyyah held that ignorant individuals are not required to make them up. According to the majority opinion, which is more cautious, you must make up what certainly absolves you or predominantly absolves you, to the best of your ability.