Missing invoice in gst

sir, in mar'20 gstr-1 file of Rs. 169155/- and payment made in gstr 3b Rs. 279412/- which is excess payment of rs. 110256/- (SGST + CGST) and in apr'20, 02 nos of invoice rs. 110256/- (SGST + CGST) has been shown in gstr-1 and gstr-3b of apr'20 shows as nil. Now department has sent a notice asking to pay the Rs. 110256 ((SGST + CGST) + interest till now which is huge amount.  Procedure may be wrong but liabilities has been paid, so replied  to the dept that the amount has already been paid but they still asking for the amount. What to do now Please reply sir