Dear Krishan Sharma,
You can raise a supplimetary Invoice or a Debit Note for differential tax. Please note, Assessing authority will also impose penalty and levy interest for non submission of C form within prescribed time. Further, it seems that your customer had suppressed the facts and acted on these suppressed facts that he was entitled to purchase the goods on concessional rate of tax under CST Act. Under CST Act this type of activities are defined as offence. You can bring this issue to the knowledge of the HVAT Authorities if your customer is not willing to pay the differtial tax along with interest and penalty, if levied/imposed by the HVAT Department. But first of all, please try to sort this matter mutually and harmoniously.
Best Regards,
Pradeep Khatri