For Line Item entities Opportunity Products, Quotes Products, Order Products or Invoice Products, you can chose what type of Discount you want to give out.
This is a simple Organization-wise setting that you’ll need to set to define how Discount should be given on the Line Item level.
Navigate to System Settings and under Sales tab, find this setting
You can chose either…
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Discount Settings for D365 Sales Line Items – Line Items or Per Unit?
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