Unmark an order as 'paid' - order marked as paid incorrectly

[unravelled]

When editing an order, a new item was added that created an amount that the customer needed to pay. The customer paid the outstanding amount directly into the business bank account but when marking the order as paid on Shopify, it marked the entire order as paid instead of just the outstanding amount. Now it seems as though the customer has paid double for the order when in fact he only paid the correct amount. How do I fix this?