Redownloading of orders from Shopify that are "partially refunded"

If a customer calls and amends their order, ie removes an item or selects a cheaper alternative, we amend the order in Shopify and then process the part refund to the customer within Shopify. All Shopify tasks are then completed. Just like if we had added items to an order, we then redownload the order in StoreFeeder, which usually works fine, but if an order is "partially refunded" in Shopify, it gets deleted in StoreFeeder (standard when redownloading an order) but doesn't then pull in successfully. This has resulted in a number of orders not being dispatched on time and essentially being forgotten about :( We wish to be able to redownload "partially refunded" orders successfully.