How can I fulfill an order after a partial refund?

There are times when we refund a coupon code or a shipping discount as a customer appeasement before an order ships. The order still ships and the customer still receives the order, we just partially refund against their purchase to offer them service. In my experience, the partial refund is then taking the item off of the order. Is there any way around that? We still want to fulfill the order and send tracking information to the customer. I haven’t ever worked with a system that takes the item off of the order for a refund. A refund and return are not the same transaction. Anyone have any thoughts or tips on this? I’d love to figure out a way to partially refund an item/order and still have the item active on the sales order.

Thank you