The "Mark Order as Cancelled" option will stop the follow-up email from going out to the customer only if the follow-up email has not yet been sent out.

You will want to mark an order as cancelled when a customer has cancelled their order or if you have to cancel their order due to backorders or being out of stock.

You don’t want someone to leave a review on a product they won’t receive. However, you will need to mark the order as canceled before the follow-up date.

If the follow-up email has already gone out, you can still mark the order as cancelled if you prefer for your reference.
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