Rule 86B - payment missed - Goods and Services Tax - GST

Dear All, One of my client has not paid 1% of Tax through Cash Ledger where he is liabile to pay through Cash ledger for the FY 2023-24. Tax amount is Rs.1.00 Lakh. His GSTR-9 was filed without adhering to the rule. Now he wants to pay along with interest however he would like to know once he pays the above amount through Cash Ledger, whether equivalent amount of tax he is paying through cash ledger can be recredited to his Credit Ledger since the payment now he is about to pay will lead to double taxation? Please advice.