Hi there,
I am having the same issue with my store.
I have been using a bundle app for some time that auto-generates bundle discount codes. However on three separate occasions (only three so far, out of about two-dozen), when the buyer has proceeded to the payment screen to complete their bundle order, the discount code gets “lost” and the discount is no longer applied when they go to pay. It shows in the cart, but not in the payment screen. I tested and it happened to me as well, even though on past tests the discount was applied at checkout for me without issue. All of these issues occurred within the month of October 2022. Most customers don’t have the issue, but I would very much like to resolve the problem and hope Shopify is working on a solution to it.
Thank you.