Hey @cs-sf,
Thanks for reaching out and Welcome to our Developer Community!
After using the inventory_remove mutation to correct the inventory quantity, you should be using the order_update_fulfillment_status mutation to set the order and its line items to the fulfilled status. When a line items status is set to fulfilled it shouldn’t be allocated.
If you haven’t already, I’d recommend checking out our article on the Order Flow via the Public API.
Please let me know if you have any questions or concerns.
Best,
RayanP