When Dear integrates with Quickbooks online, it reads the payments from Quickbooks, but not applied discounts. The suggestion from support was either force balancing payments in Quickbooks or making adjustments in Quickbooks and Dear(which probably not work).
If you are going to tie Dear to an accounting system, the data needs to be accurate on both ends. Reading applied discounts to invoices from Quickbooks should be no big deal and is a regular part of business. Many businesses do not know until after billing whether the client will receive a particular discount.
Dear should read APPLIED DISCOUNTS AT PAYMENT from QBO or Xero if it is going to track payments on invoices.