Hi Kallol,
Generally at the time of go-live we discuss all these points with business and come to an amicable agreement. So, you can very well discuss with client and explain the constraint. As mentioned by TW and Siva, you have to create returns or credit memo request without original Invoice reference. In the return document/credit memo request keep the original document number in the PO field.
If incase, your client wants that number to printed on the credit memo document then you may have to change the logic or add the logic in output program accordingly.
Regards, Sai Krishna.