A question we hear a lot: "When a customer accepts an upsell, is the original order edited or is a new order created?"
No new order is created. When your customer accepts an offer, the item is added to the existing order via a Shopify order edit:
One detail you will notice in the order's payment history: there are two transaction IDs, one for the original payment and one for the upsell charge. That is how Shopify processes the post-purchase payment and cannot be avoided. Both transactions belong to the same order, and payouts and reports treat them as part of that order.
Because the order is briefly held open for the upsell decision and then edited, systems that pull orders immediately after checkout can grab the pre-upsell state. If your ERP or fulfillment tool misses upsell items, read ERP and fulfillment integrations (Billbee, JTL and more) and On-hold orders and release timing.
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