Hi,
I understand the issue. By default, when you add a new item or change amount in the order, you need to click recalculate to update the total price. It already has the function to get the total amount from the original order and no need to recalculate. The total amount is not calculate while making the duplicate but simply copy the amount from the database. If you change the order total in the database and if the Copy Old Price option is enabled, the amount will be copied whether it correct or not.
If you are using old version of woocommerce please update it and i would suggest to enable “High-performance order storage” from the woocommerce setting (Advanced>Features)
Thank you