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I would still send your response to the CP2000 and maintain your documentation. If the IRS makes the proper adjustment
from your CP2000 response, then you can simply move on without any additional hassles. However, if the IRS doesn't make the proper adjustment from your CP2000 response, you may want to hire a CPA, EA, or tax attorney to help you. These licensed tax professionals can deal with the IRS in your behalf, and they may be able to help solve your problem more expeditiously.
The notice of deficiency gives you 90 days to file a Tax Court petition. If the matter isn't fixed within the 30 day period prior the 90th day, I would recommend filing
the petition. You don't have to hire an attorney to file the petition, you can used this form
(http://ustaxcourt.gov/forms/Petition_Kit.pdf) to file the petition on your own behalf. After the petition is filed, the case will go back to IRS appeals. IRS appeals is usually a good place to get issues like this resolved.
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