Does a Sixth Schedule Autonomous Councils have a separate electoral roll.

The Sixth Schedule to the Constitution of India,  has a long chequered history dating back to the Colonial era. Better go through Articles 244, 275 (1), 280, 73rd Amendment, and the 125th Amendment. There is also the Bengal Eastern Frontier Regulation of 1873, and the recent Citizenship Amendment Act of 2019 does not apply to these areas.