Pre-Order Setup – Pay 40% Online, Pay Remaining Balance In-Store (POS) – Issues with Refunds & Exchanges

Hey Shopify Devs,

We need to set up a pre-order system where customers pay 40% online and the remaining 60% in-store via POS.

We couldn’t find a way to remove a discount after the pre-order is placed, so we created a Shopify Flow that adds a custom item (“Rest of the Payment”) with the correct amount. It works but makes refunds and exchanges difficult to manage.

Has anyone found a better way to handle this setup while keeping refunds and exchanges simple? Any app or workflow suggestions?

Thanks!