Gst Notice for payment of tax on duplicated invoices

I have a client where his invoices are duplicated when filing the return GSTR-1 In FY 17-18 and because of that he adjusted the tax amount on duplicated invoices and paid the tax in GSTR-3B which is to be paid and on top of that we failed to file the credit notes for the invoices duplicated within the time limit and even this issue was went unoticed while filing GSTR 9 of FY 17-18. After 4 years now we have received the notice from the department regarding the discrepancies.

Please provide the resolution for the same