Let me provide additional information, @mkm2.

The Vendor Credit and the Bank Deposit will show up on the Unapplied Cash Bill payment up until the Date to when they were linked. Since the transactions are already linked with the Bill Payment. 

Let's make sure that you included the bill payments date when you run the Profit and Loss report. This way the transactions will remove from the Unapplied Cash Bill Payment Expense Category.

To learn more about running and customizing reports in QBDT, you may check this article: Understand reports.

Reach out to me if you have any other concerns or questions about QuickBooks. I’m here to answer them for you and make sure you’re taken care of. Have a good one.