Hi @facialflex
This is not a clone issue.
On any order, you can edit the order by first hovering over the product and selecting edit. Once that is enabled, you can edit the items quantity, price, add new products, change shipping and more. This is just how WooCommerce works.
Here is some images showing you what to do:

Here I am showing you the “Edit Item” that displays when hovering over the item in the order
This gives you more options, like removing the product, adding products, adding fees, adding shipping and to save the edited order:

Hope this helps you using WooCommerce.
Thank you. I’ve realised what I need to do is to delete the items and/or shipping copied over in the basket and then add the new requirements. If I just increase the quantity from the old order it remains at the old price.
Understand. The “Recalculate” button should update the order total in that case. Or add a “fee” to alter the price as you need it.