How is a partial refund calculated when only some items come back?

The order-level discount gets spread across every line item in proportion to its price. So each returned item is refunded at its discounted price, not the price on the product page, and tax is worked out on that discounted amount. Free shipping means there's nothing to refund there. To check by hand: take the discount, multiply it by (returned items' price ÷ total of all items before discount), and subtract that from the returned items' price, then add tax at your rate. Pennies can still be off because each line gets rounded separately. If it's still way off, look at the order's details page, it usually shows the discount allocated per line.