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There is no need to file a petition with the tax court as long as you plan to file your return and pay what you actually owe.
A petition with the tax court would only be filed in situations where the IRS assessed a tax that you disagree with, but you have nothing to change on the return that they filed on your behalf. You have indicated that there will be changes once you file your return, so that is all you need to do at this point.
Once you file your actual return and send it to the IRS and pay the tax that you actually owe, then the IRS will close their files on this, unless they find something in your return which they would disallow. If that were to happen you would again receive another notice of a proposed change to your tax return. At that point if you disagreed with their decision, you might want to think about filing an appeal, but that would not be done at this point as you have yet to even file your return.
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