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Hello and thank you for using Just Answer,Your tax professional should be able to advise on your protest rights but, you may dispute an assessment received by the Department or any provision of the Tax Administration Act in one of two ways: 1) by filing a written protest with the Secretary of Taxation and Revenue, or 2) by paying the tax liability and then filing a claim for refund.You can request to have the penalties abated but not the interest. If they choose to allow the abatement a notice will be sent to you. As far as I can see that would be your only help because of the deadline being missed.