The Goods and Services Tax Network (GSTN) has introduced an important change on the GST Portal concerning taxpayers who want to challenge demand orders showing "NIL" or "Zero" demand.
The change addresses situations where a taxpayer disputes the underlying liability, but the demand order reflects no outstanding amount because the taxpayer had already made the required payment before the demand order was issued.

Official copy of the Advisory is as follows
Enabling Filing of Appeals in Cases Involving NIL or Zero Demand Amount – reg.
In cases where a dispute regarding liability exists but the demand amount is reflected as "NIL" or "Zero" in the demand order, and payment has been made by the taxpayer prior to the issuance of the demand order, the previous validation restricting the filing of an appeal against such demand orders has been removed from the GST Portal. Accordingly, taxpayers are now enabled to file an appeal in Form GST APL-01 against demand orders reflecting a NIL or Zero demand amount.
Taxpayers facing the above issue may now file an appeal in Form GST APL-01 against such demand orders.
In case of any query or difficulty while filing the appeal, taxpayers may raise a ticket with the GST Helpdesk for assistance.