Hi @Bpkeeper,

Let's review first all the transactions of your customer to check if there are any other outstanding transactions. You can consider this as one of the reasons why it's still showing a negative balance after recording a refund check.

To do so:

1. Go to Customers.
2. Select Customer Center.
3. Find and open your customer's profile.
4. Under Transactions, select All on the Date menu.

If there are still outstanding transactions or amounts on the list, you can create a new refund check to resolve it. But if you're unable to see any outstanding transaction, you may want to consider running the utility tool.

From there, QuickBooks will automatically any issues on your company file which can be the reason why your customer still has a  negative balance. That being said, here's how you can run to tools:

1. Go to File.
2. Select Utility.
3. Tap Verify Data.
4. Hit OK.
5. Go back to File.
6. Select Utility.
7. Hit Rebuild Data.
8. Click OK.

I've got you this article for more information about the tools: Verify and Rebuild Data in QuickBooks Desktop.

Please let me know how it works in the comment section down below. I'm glad to lend a helping hand.