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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
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the chosen customer's transactions.
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Find a correction block
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at the end of the page.
Specify needed amount and
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leave a comment for client
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You can also set a negative amount to remove credits from customers account.