It's easy to remove a discount from an invoice if needed. You can remove the discount from the entire invoice or from individual line items.
 

To remove a discount from the entire invoice, simply click on the X next to the discount.

By default, a discount will be applied to the entire invoice. To remove a discount from an individual line item, open the line item by clicking on its dropdown arrow and selecting Edit. Then toggle the Apply Discount setting off and click Save Item.

YES. If it has a discount code, a max number of uses set, AND was applied by a client (not manually by you), one use of that discount code will be restored when you remove the discount from the entire invoice. For example, if a discount is maxed out because it was applied via the code the maximum number of times, removing the discount from one of the invoices will restore one use and make it valid again.

Unfortunately, QuickBooks only allows discounts to be applied to the entire invoice. This is outside of Dubsado's control. If you have synced your Dubsado account with QuickBooks and need to remove a discount from only a few line items, the workaround is to remove the percentage discount entirely and apply a fixed amount discount instead.