Since orders going to multiple addresses begin with a single checkout, with all of the shipping and tax detail included in a single order, the actual transaction or transfer of money stored in Shopify is associated with this order.
The process to refund an order or part of an order going to multiple locations has two steps:
1. Calculate the refund amount from the recreated order(s). These orders will be tagged with "ms_fulfillment_order", alongside a reference to the order that is was created from in a tag starting with "created_from_".
2. Navigate to the original order (in this example case #1001) and issue the refund for the calculated amount:
You may also want to cancel or refund portions of the recreated orders in order to keep your reporting and inventory accurate. So, for example, order #1001 was placed and had 2 addresses, which caused order #1002 and #1003 to be created. If order #1002 arrived damaged, and needed to be refunded, first go in to order #1002 and refund the full amount, specifying that the customer does not receive the notification. Then, in order to actually refund the customer's card, navigate to to order #1001 and refund the portion of this order calculated from the refund amount of order #1002, ensuring that the customer does receive a notification by keeping the "Send a notification to the customer" box checked.