How does 'Advanced Product Options' by Mageworx work?
When a customer adds a custom product to the cart then 'Advanced Product Options' app immediately creates a new product in Shopify dashboard for that customer. So dynamically created new product will not get discount from the Wholesale All In One app because you didn't define discount for new product in the wholesale app. Ultimately, customers will not get discount for that specific newly created product.
We need to choose the 'Combined Items' option from the 'Advanced Product Options' that doesn't create new products when proceed to checkout. Please look at the below screenshot:
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