I think your question is can we raise a single Credit Note (or Sales Return) for items which were sold in multiple Invoices ?.
As for uploading details in Portal, it asks for an Original Invoice Number pertaining to the Credit Note issued.
This has created practical difficulties for the traders, as in real life, he will receive sales returns of items, which would actually be pertaining to multiple invoices. And he has to generate separate credit notes for each original invoice
However GST Council had sounded out that they are proposing an amendment to enable mentioning of multiple original invoice numbers in a single credit / debit note. The exact date of implementation is yet to be known
Till such time, it is advisable to issue separate credit note for different invoice numbers