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Thanks for joining this thread, @jclose.
To help you with regards to seeing a per-line-item Discount feature be added to invoices via the QBO API, let me route you to the best support available. We have a forum called Intuit Developer where you can get an answer from one of the experts handling integration like API, developments, and other related concerns.
I'd suggest posting your situation on their forum as they are the best gurus that can help you with your concern. I'd be glad to guide you on how:
You'll want to check these articles to help manage your invoices and other sales forms in QuickBooks :
Please know that you're always welcome to post if you have any other concerns with adding discounts to invoices. Wishing you and your business continued success.