1. Create a Supplier Refund when you receive a refund.
2. Then, when you have to create a Supplier Invoice, create it to its full amount.
3. When the time comes to pay your Supplier Invoice, go to Accounting > Supplier Payment and create one. As soon as you select the supplier in the field, the Supplier Refund and the Supplier Invoice will appear in the Credit and Debit sections. This is where you have the chance to pay the amount of the invoice minus the amount of the refund by allocating their full amounts. You can even allocate those amounts partially according to the situation (eg. you only want to use the full refund amount to pay half of the invoice).

More on this here: https://www.odoo.com/forum/help-1/question/excess-payments-on-invoices-in-v7-40371