If you offer ISR invoices you can adjust the invoices if items are returned or if you want to adjust the positions on the invoice. You can do this inside wallee by creating refunds on those line items that you want to have removed. This will replace the invoice with the new line items.
Please note there are several shopping carts like Magento where you can not issue refunds for unpaid invoices. In this case you do have to create an the refund directly inside wallee.