Headless Build, Unable to edit Orders

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We are using a headless build and using the API to run our store but as soon as someone presses checkout on our website, it goes directly to the Shopify checkout flow which has not been modified. 


Right now, we are unable to edit orders in Shopify which is causing a lot of problems for our customer service team. We'd like to be able to do so. 


We've been told that we have to make sure our checkout is up to date (which it is) and that it is because we are using the API (which we are but before the checkout experience, not during). I'd love more information on what we can do to ensure that we can edit orders.