3.
Ideally, your client should have raised debit-notes u/s 34, disclose the same in Form GSTR-1 and pay the differential tax liability through corresponding Form GSTR-3B.
Now, as your client has paid the differential tax liability through Form DRC-03, following process may be followed as a practical solution:
A. Raise debit-notes u/s 34 and disclose the same in GSTR-1 but do not pay the differential tax liability while filing corresponding GSTR-3B. End customer can claim ITC against these debit-notes.
B. Once notice for the differential tax liability is issued by Dept. under Rule 88C, furnish reply u/r 88C(2)(a) explaining the fact that the differential tax liability is already paid by you by giving the details of Form DRC-03 used for the same.
C. After submitting above-said reply, please also meet concerned officer, explain the bona fides of your client's conduct and also explain him that any recovery u/s 79 now will amount to double tax-payment.
I do hope that concerned officer accepts your reply & explanation and do not proceed for recovery u/s 79.
These are ex facie views of mine and the same should not be construed as professional advice/suggestion.