The only replacement method that Amazon supports is when the buyer chooses to have a replacement sent when putting in a return request. In that case, once the buyer sends back the first package their pending $0.00 order becomes a regular order which you ship at that time. It sounds like you sent a replacement after receiving the item back instead of using the official replacement method outlined above. The issue here is that Amazon will refund the order after 48 hours (seems to usually take about a week in reality) if you don't refund the return. The only way to keep them from doing the refund is to do a partial refund on the order, but the interface won't let you refund a small amount. You could do a flat file upload instead of going through the regular interface to refund a small amount. (I'm not sure what the minimum has to be to prevent Amazon from doing the auto-refund in full. $0.01 used to work, but I've heard that it doesn't any more. You might want to refund $1.00 or so just to be on the safe side.) To use the flat file upload method at https://sellercentral.amazon.com/order-reports-and-feeds/feeds/adjustments# you will have to have a Professional Seller Account. Also keep in mind that if the buyer was to open an A-Z claim stating that they didn't receive their refund that you would lose. In the future, never send a replacement on a returned item unless it was put in as a replacement request through Amazon's return portal.