QB Issue Resolution:

The use of an SO is a Fulfillment process, so it considers the discount has already been Fulfilled.

I teach four different ways to control pricing for customers. If you can’t use Price Levels, I would suggest you cannot use the discount item TYPE for this on the SO without overriding the info on the Invoice to manually include the Discount item. This is called “an item that calculates;” it calculates on the item above it (or a subtotal item); and of course, does not provide for Qty, for fulfillment purposes.

Does this seem different than prior? Or, perhaps you were using Group Items, before?

Resolution for Issue 'Issue of discounts on a sales order showing up on the associated invoices?' available: Yes (Solved).
Source: Intuit Community forum.

Issue of discounts on a sales order showing up on the associated invoices?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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