Are you wanting to refund or charge the customer for the difference in price? If yes, you can send them a draft order with the difference in cost (if higher) or you can offer them a partial refund (if lower) from within the order itself.
The order details can't be altered without taking actions like that. It is required that the order reflect the transaction that happened in its entirety. This is both for your tax purposes, but also for the customer if there is any issues or claims against this order in the future.
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