How do I pay off an invoice which has been offset by a lower figure being paid into our account?

We used a 3rd party to do an R&D claim. We received a rebate on corporation tax as a result. The company invoiced us for their services and paid us over the balance of the rebate less their invoices. I have entered the invoices in order to reclaim the VAT but I cannot pay them off as their isn't anything to pay them off with and I can't allocate it to the corp tax ledger.