Discounts show in the cart but disappear at checkout

Short answer: the customer probably reached checkout without using the cart page checkout button, for example with Buy it now, an express checkout button (Shop Pay, Apple Pay, Google Pay) or a direct checkout link.

Cart after the code: each line shows the original price struck through and the discounted price

What your customers see on the storefront.

BSS B2B Solution shows B2B prices and discounts in the cart, then applies them when the customer clicks Checkout on the cart page. Paths that skip the cart can skip the modules below.

Module	Shown in cart	Applied when checking out from the cart page	When checkout skips the cart page
Custom Pricing, Price List, Volume Pricing	Yes	Yes	Designed to hold at checkout. Test on your theme.
Buy One Get One	Yes	Yes	Can be missing
Discount Code	Yes	Yes	Can be missing
Extra Fee	Yes	Yes	Can be missing

Cart with the Extra Fee table open under the product

What to do

Make sure the app embed is on. When rules are active, the app hides Buy it now on the product page, but only if the embed is loaded.
Test the full path as a customer: add to cart, open the cart page, click Checkout.
If your theme adds its own express checkout buttons to the cart or cart drawer, consider hiding them for B2B customers.