When creating an RMA to handle items that your customer has issues with, there are two options to choose for each item. You can select that the customer is Returning an item to you for a refund, or you can select that the customer is Not Returning the item, but that you're issuing a partial refund to account for the issue. These options have different financial impacts in WholeCell. Here's how they work:
If an item is being returned on an RMA, the refund amount you enter for that item is stored in the RMA itself, but is not reflected anywhere else in WholeCell because the item is coming back from the customer. Once marked as "Received", that item is removed from the Sales Order it was on.
If the item is not being returned, the refund amount is added as a cost on the item itself, because the customer is keeping it and the financial impact is final. This cost can be seen on the RMA or on the individual inventory item's page.