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ANSWER: At this point, you need to file the past tax returns that were not filed. Then you should have information from the IRS that explains that you are in the process of fixing this issue. Often, this is enough to overcome the deficiency. Otherwise, the safest way to do this, without risking losing the cost of the naturalization, is to wait until you have completed the filing of the back taxes and then file for naturalization. You do not have to wait the two years. Just file the back taxes and then file for naturalization.
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