Thanks for your reply. I am in the process of contacting support regarding this matter.
I believe both Amazon Pay and Shop Pay are caused by the same reason.
the following is my guess.
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For a period of time, Shopify will transition the checkout to /checkout/c/ for a particular device environment. (maybe for AB testing or something)
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When using an external payment service, Shopify transitions once from /checkout/c/ to /checkout/. (because the redirect URL must be matched)
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Product information is copied when transitioning from Checkout/c/, but information such as line item properties or cart attribution is missing at that time. (I have confirmed such behavior)
I am 100% sure this is a problem on Shopify’s part. The workaround now is to turn off Shop Pay for specific devices, but this would not be practical. We don’t touch the checkout page so the workaround is just about off. Let’s wait for the fix.