Create a non-printing manual check entry for 0.00. Apply it to all credit notes and invoices that should be matched up but are not. Posting this entry will set the Current Amount of these transactions to 0.00 and thus remove from outstanding transactions reports such as Open Payables.

The same procedure works just as well for negative invoices in addition to positive.

If the invoices and credit notes do not net to zero, it is likely that adjustments were posted (perhaps incorrectly) against an invoice. You would have to post adjustments against transactions (instead of cash) to clear them all out.