I'm having the same issue something must have changed.  I perform Make Deposits and any Credits/Refunds issued along with Sales Receipts would show so I can apply to a single deposit. As an Amazon Seller deposits come in batches so you have to show which orders were in a deposit along with any refunds you issued. It's just not working any more like used to. I hadn't done a refund since December so not sure when it changed.  Now i have to list a separate credit/check in the account and manually note/reconcile against the actual deposit from Amazon. Why why why Quickbooks why change something that was not broke. Annoying.