You can create a credit memo to remove a credit balance or remaining advanced fee funds in a client account. Inside the case under Case Billing > Invoices, click the 'Create New' button and select 'Credit Memo'.
Next you'll select the associated party and enter the credit balance or advanced fee balance in their account. You can either Save it (which removes the balance and records it) or Save and Send (which does the same thing in addition to sending them an email with a PDF of the credit memo). If you choose the Save and Send option, you can customize what the body of that email says by going to Manage Firms > Billing Settings > and scroll to this box (screenshot). Make sure to click Update Firm after you do.
Note: The credit memo does not return the actual funds. You will need to process the refund via the payment method you accepted.