Each individual item on the invoice is set up to be 'Is Discountable - Yes or No'.  If you uncheck the box to make an item not discountable, any Discount Percent or Discount Type added to the invoice will not be applied to those individual items.  To have a discount taken, you must go into each item and re-check the 'Discountable' option and resubmit the invoice.

When an item is listed as discountable:

When an item is listed as not discountable:

Result on an invoice where the discount is applied to a discountable item:

If a discount amount is entered, the amount will be deducted from the invoice.   

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