The cleanest option is to cancel it in your store. We automatically pick it up as a cancellation and it stops counting toward revenue, without deducting that order's product costs from you.
If the order was wrong because of a discount or an incorrect amount
The recommended approach is to cancel it and create a new order with the correct products and amounts. The new one is the one we'll calculate; the cancelled one stays only as a cancellation.
If you can't cancel it in your store
As an exception, you can neutralize it by entering an additional fixed cost for that order's net amount, with the start and end date set to the order's day.