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Firstly, please confirm that you did not disable adding bundle items as separate line items to bundle orders in your app settings.
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If the above app setting had not been disabled, then the reason may be that this particular order was marked as uneditable by Shopify.
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This means Shopify will prevent both the app and even the merchant to edit the order (to add the bundle items as line items).
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Learn how to handle this Shopify limitation by reading: Handling uneditable orders
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