Eway Bill generated by mistake

Dear Professionals,


Please guide for the below case study.


For the FY 2018-19, my Client's Turnover as per GSTR-3B & Books is 10 Lacs(Assumed).He is involved only in interstate sale of goods.The Turnover as per the E-Way bills generated is coming to 11 Lacs.(Extra way Bill generated twice for same invoice by the client)


In April-19 he received a notice(DRC-01) from the department u/s 73 for payment of differences of output tax coming as per returns and way bill. 


The notice had a demand of CGST and SGST on differential of 1 lacs instead of IGST. The same was also paid by the client under the wrong head SGST and CGST.


Now the point is that the notice amount has been paid under the wrong head and the extra way bill was also generated by mistake.


How to proceed in above case.