In Core, you can easily apply discounts while creating an invoice. Check out this article for details: Applying discounts to invoices.
If you want to apply a discount after the creation of an invoice, you should use the Credit or Write-Off payment methods in the Payments screen. Just use the discount amount as a payment on the invoice using one of these pay methods. Core reduces the balance on the invoice by this amount and it records as an expense in the expense account. The client now only needs to pay the balance amount using whatever method they want, such as credit card. Check Core Help Center for details on credit payments and write-offs.