Is the brownish discharge before the menstrual period considered menstruation that necessitates making up missed prayers, and is it obligatory to be certain of the emission of odorless and soundless flatulence?

Brownish discharge is considered menstruation if it occurs during the habitual period. If the brownish discharge occurs outside of the habitual period, and you avoided prayer at that time, there is a difference of opinion regarding the obligation to make up these prayers, and the view that there is no obligation to make them up is strong. As for the prayers you performed while brownish discharge was present during your habitual period, thinking it was not menstruation, you are not required to make them up. One must be wary of obsessive whispering (waswasah) and turn away from it, not paying attention to it unless there is absolute certainty that something invalidating ablution has been discharged.