QB Issue Resolution:

I would Receive the Refund for the CT and deposit it to a Contra account. That will clear the Receivable.

 

Then, I would Pay the GST from the Contra account. That clears the payable.

Resolution for Issue 'Balance Owing for GST at year end – Canada Revenue Transferred Balance from a CT Refund' available: Yes (Solved).
Source: Intuit Community forum.

Balance Owing for GST at year end – Canada Revenue Transferred Balance from a CT Refund: 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.

Support for Contra Account
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Error Recovery for Contra Account [Canada]
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