When you try to edit an order from the orders tab, the order will need to move to your cart. In order for the order to move to your cart, everything will need to be removed. This is why when you edit the order you get this message.
This message simply means you cart will be erased so your order can take it's place. The order will be moved into the cart for you to make edits. This does not erase your order or remove any items from the order.