How to manage updating all tax returns following a discovery that I'm not entitled to rental real estate loss?

According to a letter from NYS Department of Taxation and Finance, it seems we are not entitled to take a rental real estate loss according to IRS Passive Activity and At-Risk Rules for a tax return 3 years ago.

As I have been filing taxes through TurboTax for the past 7 years, this caught be by surprise as it seems TurboTax should not have allowed this. What can I do to remedy this for the tax returns filed from the last 3 years? Also, is this a "bug" in the TurboTax software? All suggestions welcome. Thanks!

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