I appreciate the details you've given, @SMcKee.

Given that you already have credits on the bill, all you have to do is to apply the credits upon paying the bill. I can walk you through how to achieve this.

You may follow these steps below:

1. From the Banking menu, click Make Deposits.
2. If the Payments to Deposit window appears, click OK.
3. In the Make Deposits window, click the Received from drop-down and choose the vendor who sent you the refund.
4. In the From Account the drop-down,  select the appropriate Accounts Payable account.
5. In the Amount column, enter the actual amount of the Vendor check.
6. Enter a memo, check number, payment method and class.
7. Click Save & Close.

Once done, you can proceed with linking the deposit to the bill credit. 

To do that:

1. From the Vendors menu, select Pay Bills.
2. Check the Deposit that matches the Vendor check amount.
3. Select Set Credits and apply the Bill Credit you created earlier then click Done.
4. Click Pay Selected Bills.
5. Select on Done.

You may also refer to the steps number 1 & 3 in this article: Record a vendor refund in QuickBooks Desktop.

If you need further assistance in performing this procedure, feel free to reach out to our Customer Care Team. They have the necessary tools that can guide you through the steps.

That should get you on the right track. Please let me know how that works for you. I'm here provide you additional assistance if you need anything else. Have a good one.