Shopify stock sync

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I'd like to sync the inventory I manage in my administrative software with the Shopify inventory using APIs. I have come to think that I would have a problem when an order is completed, when the "fulfilled order" button is pressed, it will subtract the stock obviously, however, in my system it is billed separately where the inventory is also subtracted, so the same product would be subtracted twice. Any ideas to fix this?

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