If you create a credit note against the invoice as you normally would, but then have one line as minus Net + VAT and the other line as just Net. This will give a Net 0 credit note, but then leave the VAT as the credit note total. Similar to the attached image:
When you click to save the credit note, it will give you the option to either create a new transaction in the bank account, or you can keep the credit on account for future use.