If the check was written in Transactions > Bank > Write Checks it will not be affecting your A/R account and so will not affect the balance in the Financial tab of the customer account.
To correct the balance:
- Create a Journal Entry: Transactions > Financial > Make Journal Entries
- Debit the A/R account for the amount of the check
- Put the customers name in the Name column
- Credit an account according to the company
- Accept Customer Payment:
- Transactions > Accept Customer Payments
- Select the Customer
- In the Apply tab: Invoices subtab select the Journal Entry
- In the Apply tab: Credits subtab select the Payment
The balance will be accurate and the journal entry will be attached to the overpayment.
Note: This should only be used if the check has already been issued without using the refund method process. Normal Process would be to use Issue Refund to customer.