The Tax Penalty Amnesty shall not apply and no refund or credit shall be granted of any penalty if, prior to the time the taxpayer makes a request for tax penalty amnesty pursuant to Section 21.12.5 of this article, the penalty has been paid by the taxpayer. The Tax Penalty Amnesty shall apply to tax penalties being challenged administratively or through litigation provided the tax penalty has not been paid at the time of the application and the tax otherwise qualifies under this article, provided the Tax Penalty Amnesty does not result in a refund or credit.