QB Issue Resolution:

If the refund is a result of filing vat then in Vat history you will find the vat filed period you have filed and on the line of the entry locate the Record|View payment, select record on the line and a window will open with refund selected.

What ever you do do not use the Blue Record a Payment button top left.

Resolution for Issue 'I have received a refund (repay) of VAT paid into my business bank account – how and where do I enter this please. Do I raise an Invoice and then pay it off?' available: Yes (Solved).
Source: Intuit Community forum.

I have received a refund (repay) of VAT paid into my business bank account – how and where do I enter this please. Do I raise an Invoice and then pay it off?: 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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