Waiver of penalty for late filing of GSTR 3B but unable to file

My client try to file GSTR 3B of August he has input credit same is
available in electronic ledger and offset the liability payable submitted but penalty calculated 6600 asking for payment of same on the next day Govt announced waiver of penalty, but while e-verify the return it asks for clearing of liability but in credit ledger he has excess amount. please show the way forward, due to which we unable to file September and October returns also?please help us to solve the issue!