First, create a $0 item, something like "Shipment returned". Make sure it has the same weight and dimensions as the bottle size. (If you are using Revel, you will need to make sure that this item is also on Revel so the order flows through)

Use the Customize Order option to remove the returned bottle(s) from an order. Add the item called "Shipment returned". Save the order. On the following screen it will show you the amount to refund, which will be the bottle amount, less the shipping.