I'm here to guide you on how to clear and link the check to the customer's open credit, @sarah17!

Did you record the refund through Check using the following steps below? When recording a refund using Check, you'll have to debit Accounts Receivable for the amount of the customer's open credit to offset the overpayment.

1. Select + New.
2. Select Check.
3. Select the customer you want to refund from the Payee ▼ drop-down.
4. From the Payment account ▼ drop-down, select the bank account where you deposited the overpayment too.
5. On the first line of the Category column, select an Accounts Receivable.
6. Enter how much you want to refund in the Amount field.
7. Fill out the other fields as you see fit, then select Save and close.
   

Anyhow, you can edit the transaction using the steps above. I'll show you how.

1. From the left menu, select Expenses, and choose Expenses.
2. In the Expense Transactions window, find the check to edit.
3. Under the Action column, select View/Edit.
   
4. Update the transaction as needed.
5. Select Save and close.

Once done, here's how to link or apply the refund to the customer's credit.

1. Select + New.
2. Select Receive payment or Receive invoice payment.
3. Select the same customer you used for the check.
4. Fill out the other fields as you see fit.
5. Under the Outstanding Transaction and Credits section, select the checkbox for the check and unapplied payment.
   
6. Make sure the payment is equal to the open balance, then select Save and close.

You can refer to these articles for more insights about handling customers credit or overpayment in QuickBooks Online: 

• Record a customer refund in QuickBooks Online.
• Handle a customer credit or overpayment in QuickBooks Online

Lastly, when it's time to reconcile your account, it will show the received payment, as well as the Check you sent to your customer. It will compensate to the actual amount of the invoice.

Keep in touch with me here should you have any additional questions or concerns. I'm always available to help.