...
As Admin, you can always correct Cutomer's balance.
Here are the steps:
Open "Manage customers" page in Admin backend (yoursitename /exec/manager/customers)
In column balance, find a "+" button near customer's balance and press it. You'll be forwarded to the chosen customer's transactions.
...
Find a correction block at the end of the page.
Specify needed amount and leave a comment for client
...
You can also set a negative amount to remove credits from customers account.