If you do not wish to credit the whole of an invoice, it is possible to raise a partial credit note.
To raise a credit for a particular item on an invoice, please follow the instructions for Crediting an Invoice.
To raise a Credit for a Company
Note that this credit note has not been raised against a particular invoice, but for the customer as a whole. It is important that you go on to allocate this credit to an invoice.
To allocate a Credit to an Invoice
If there is an outstanding invoice, then you can allocate the credit to it immediately, but if the credit note is for future purchases, then you will need to wait until another invoice has been raised for you to allocate it against. The credit note you have made will wait on their account until that time.
To allocate it to an invoice, go to Accounts > Sales Ledger > Sales Accounts Query. Search in the Hot Area for the correct customer and you will see that credits and payments are shown in red, while invoice are white.
It is here that you can allocate the credit to an invoice.