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.
In order to process a refund for an order or part of an order going to multiple locations, it is a 2 step process:
1. Calculate the refund from the recreated order(s), or portion of. These orders will be tagged with "ms_fulfillment_order", along side a reference to the order that is was created from in a tag starting with "created_from_".
Now navigate to the original order, in this examples 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.