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In order to consider payment discount the payment (refund) needs to be the applying entry. If choosing an invoice, the payment discout simply gets ignored and thus the (customer) ledger entry doesn't get closed.
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Needs Votes
Ideas Administrator

Thank you for your feedback. Currently this is not in our roadmap; however, we are tracking it and if we get more feedback and votes, we may consider it in the future. Sincerely, Business Central Team