Hi Ralph,
If a credit note was posted to a vendor and not applied to a particular invoice, then indeed it will not get cleared by Period End, nor will the invoice.
You can create a zero-dollar manual check entry - make sure to not select the 'print check' option, and apply 'payment' to both the credit note and the invoice. You may want to fill the the check number field with a large numeric value so not to confuse with actual checks.
You can then post the manual check batch and the current amount of both the invoice and credit note will be changed to zero.
Of course you could always adjust out the invoice and credit note, but that may be a bit messier.