If the corporation needs to file all its corporate returns. Without doing so, you can not proceed to liquidate the corporation. Importantly, if the S corp had a loss then it should pass to you via a K-1 (Form 1120S). This loss may be able to offset other income on your individual return. Bottom line here is that you need to file the S returns which may allow losses to you personally and it will set the stage for the dissolution procedure with the state.
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You should file the tax returns by amending your personal returns and make sure they do not assess you with a tax. You can report that the corporation is being dissolved when you file your taxes each year, HOWEVER, you are not allowed to dissolve a coproration in New York if there is an unpaid tax liability...so there is no easy way around this, you must file the taxes, but since it's a single person entity you can probably do this by amendeding your prior returns.
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I suspect that we are mixing tax authorities here. The IRS (Federal tax) does not send notices to the effect that they will dissolve the corporation for failure to pay tax. Moreover, a corporation does not cease to exist if it fails to pay income tax. The tax at issue appears to be New York's "franchise" tax or the tax that states impose on you for the privilege of creating and maintaining a corporation. New York can (and will) dissolve your corporation if you fail to file the appropriate corporate franchise tax form. You can learn more about the corporate franchise tax at the following weblink:
As for dissolution, the first step is to ensure the corporation has paid all its bills. There are basic instructions available on the NYS Department of State website at:
I hope you find these answers helpful. You should understand that dissolution can be a complex process and it may be that your best alternative is to allow the tax dissolution to occur. I cannot offer any opinion on that point without having more facts about your matter.
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