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Buy nowI appreciate the complete details you've provided, @mkm2.
When creating a credit or refund, always select the same bank account that is originally used in paying the bill. Since you've used a credit card in paying the bill, let's also make sure to post the credit on the same account.
Also, let's first run the Verify and Rebuild Data tool to help us identify some data issues within your company file. Here's how to verify your data:
If you'll receive the message "Your data has lost integrity", it means there's data damage in your company file. To correct this, continue in rebuilding your data. This process will require you to back up your company file to ensure you have a secure copy of it.
In case you accidentally write a check to pay an existing bill, the two transactions won't be linked and the bill will still be in an unpaid status. To fix this, you can refer to the Bill shows as unpaid after writing a check-in QuickBooks Desktop article for the recommended solutions.
Keep me posted if you have other questions. I'm always here to help.