This is really tragic way of doing things in wrong way by Banks. After flooding of private bank on Indian Banking system they have made up their own rules and public is being harassed by many ways. Your balance can never be negative and the account should have been put to dormant immediately after 6 months.
They make balance negative for any adjustment if they get any payment to your account by mistake. But don’t worry they cannot do anything. Alternatively you can write to Bank ombudsman and Finance Minister of India.