Final answer:
The taxpayer can file an amended return by January 9, 2011, as it is within three years of the original filing date and two years from when additional tax was paid, whichever is later.
Step-by-step explanation:
The latest date on which a taxpayer can file an amended return for the 2006 tax year, when the original return was filed on April 16, 2007, and the IRS examined the return which resulted in additional tax paid on January 9, 2009, would traditionally be within three years from the date the original return was filed or two years from the date the tax was paid, whichever is later.
Therefore, the latest date for this taxpayer to file an amended return would be January 9, 2011. However, since tax laws and deadlines can change, and there could be special circumstances affecting this deadline, it is always recommended to consult directly with the IRS or a tax professional for the most current advice.