QB Issue Resolution:

To keep reporting correct, you need to create a credit memo and apply the CM to the invoice in receive payments

use an item that points to a sales discount account

or edit the invoice, reduce the amount, and explain in the memo block, save and click through any warnings (not cpa approved) 🙂

Resolution for Issue 'How can I write-off a small balance left on a customer account after underpayment of an invoice please?' available: Yes (Solved).
Source: Intuit Community forum.

How can I write-off a small balance left on a customer account after underpayment of an invoice please?: 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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