I've got nocturnal epilepsy, if i suddenly stop taking anti-epileptic drugs (200 mg, twice a day) would that effect my brain?

Potentially: Seizures are aberrant discharges of your brain so if you have seizures whether they happen during the day or night, your brain is in a frenzied state for some time and then enters a dormant type of state (post ictal). The hard part about nocturnal seizures is that since unconscious when asleep, could be happening many times. That may lead to a status condition in some people. Speak with dr.