QB Issue Resolution:

Two lines one line has nett amount positive to create vat amount , second line has net rate as negative with vat code of No vat.

Vat only is posted,

Resolution for Issue 'How do I issue a VAT only credit note' available: Yes (Solved).
Source: Intuit Community forum.

How do I issue a VAT only credit note: 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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