There is no specific section or provision under GST law to claim the input tax credit (ITC) on credit note twice, which was supposed to take only a single time. However, you may try to rectify the mistake in the GSTR-9 and GSTR-9C forms by following these steps12:
In the GSTR-9 form, you can report the correct ITC amount in Table 6 (I) and Table 7 (I), which are meant for adjustments of ITC availed or reversed in the financial year for which the annual return is being filed.
In the GSTR-9C form, you can report the correct ITC amount in Part II, Table 12 (B), which is meant for adjustments of ITC availed or reversed in the financial year for which the reconciliation statement is being filed.
You can also mention the reason for the adjustment in the auditor’s recommendation statement in Part V of the GSTR-9C form.