Yeah, this is where Quickfile falls short. Would be handy if you could add your vote to this thread.
The workaround is to go to the invoice you want to apply the credit note to, click More Options, Credit Note. Then when you have created the credit note you can go to the Receipt Hub and tag the credit note to the QuickFile CN. If you create the credit note from the Receipt Hub it doesn’t show any entries for unpaid invoices, which would be the simplest way of doing it as this is how credit accounts work.