Canceling orders through the Channel directly won't automatically cancel the respective Magento order.
In this case, you need to cancel the Magento order separately by creating a Credit Memo.
To avoid additional effort when canceling or refunding, you can configure M2E Pro to update a channel order automatically by heading to eBay/Amazon/Walmart > Configuration > Account > Orders > switch the Cancel/Refund orders option to Yes.
From now on, once you create a Credit Memo in Magento, M2E Pro will automatically pass the update to the channel.
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