Currently, we don't have an option in D365 to refund only the shipping amount. It's required some time for a goodwill refund.

There are circumstances where shipping gets delayed. But in RMA we can refund the shipping amount after selecting at least 1 item from the original order, which is not required in all cases.

Also, we can initiate the blind refund (Credit only) but in that case, we can't link with the original order and that refund not get traced further.

If we get this option in D365 RMA (Call Center), it will be good for the CS team and customer and avoid manul refunds.