Paying for items kept by a customer in a consignment order post return via API - possible?

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We're building a private app for partners which will place orders in a shopify store for $0 and mark them as paid. That order will ship to the customer. When the customer decides what they're keeping is when we'll pay Shopify for the order. Will it be possible do pay shopify directly for this (via backend/API) or will we need to use a third party?