Sales Document unapplied but showing unapplied amount zero ($0)

Your document (return, credit, payment) was not applied to an invoice.
You go to Apply Sales Documents and you see your document but you cannot apply it to an invoice as there is no amount remaining for application on this document.
You run checklinks and this does not resolve your document but fixes other documents.

Have no fear! Do the below:
Run Reconcile on the Customer from the Reconcile Receivables Amounts window (Tools | Utilities | Sales | Reconcile).
Run the reconcile on both Current Customer Information and Outstanding Documents Amounts, for the customer with the issue.

Voila!