Problem
A customer paid their invoice early and took a discount. The invoice and payment were already exported. You need to apply a discount to clear the remaining balance of the invoice.
Solution
To do this, create a Pricebook service item for the discount. Then create an adjustment invoice from the exported invoice. Finally, add the discount to the adjustment invoice you just created as a negative amount.
Create a discount task in Pricebook
On the navigation bar, go to Pricebook > Services.
Click Add Service.
Enter the name and code for the discount. You can name the service task "Discount."
Select the corresponding Income account.
Make sure the item is not marked as Taxable.
Leave the Price at $0.
When finished, click Save.
Create an adjustment invoice and apply the discount
Search for and go to the exported invoice.
On this invoice, create an adjustment invoice.
On the adjustment invoice, add the discount task you created in the previous workflow.
Set the discount task amount to the negative version of the discount amount. For example, if the discount amount is $10.00, enter "-$10.00."
When finished, click Save. This should clear the remaining balance of the invoice to zero.