Taxamo is the reporting tool for all of your transactions so flagging a transaction for a refund in Taxamo will not affect a refund to your customer.

You will need to do that through your payment service provider or shopping cart. When you call a refund request in Taxamo it marks the transaction refunded on your tax settlement report. You will also need to report all your refunded transactions to the tax authorities. If you don’t mark it as refunded on Taxamo then the report will overstate your tax obligation.

Depending on the type of the Taxamo integration the refund can be automatically updated in the tax settlement report. Check out the documentation here on how to create a refund.