I think @abctax55 may be right, the question is about 1099s (also acceptable, 1099's) and not a 1099-S.  

I don't think IRS is still issuing CP2000's for 2018 and 2019.  More likely, they did that a year or two ago, and then followed them with notices of deficiency, and then assessed the tax, and the client is just now getting around to opening the mail.  

You don't file an amended return in response to a CP2000, you answer the notice by the date requested.

If the tax has already been assessed, you ask for an audit reconsideration, if in fact there was something wrong with the IRS computation.  Otherwise you pay the bill, or ask for an instalment agreement.