If I understand you correctly, you filed an original return and 3 years later you amend that original return that lowers the amount of refund received. What will happen is you will be assessed the difference between the higher original refund and the lower amount as tax owed. Along with that will be penalties and interest from the original date of filing. The taxing authority will deem that you overstated your deductions thereby causing to large of a refund. That is why they go back to the original file date and asses tax, penalties and interest. When you file the amended return, it will show that you owe tax, you should pay the tax and the taxing authority will send you a letter requesting payment of penalties and interest. Also, depending on how much the difference is it could trigger a look by the agency to see if the overstatement of refund could be fraud and thereby assessing higher penalties.

It is important to be very accurate with deductions and refundable credits when filing tax returns. As a tax resolution specialist and practitioner that has fixed the problems of individuals who "do" their own returns, I feel it more valuable to find a competent tax practitioner to prepare and guide you through the intricacies of tax returns. Plus if they are an Enrolled Agent like I am or a CPA they can help you when issues arise.