I call BS on this.  The taxpayer has every right to file an amended return within the prescribed time limits of the law.  The IRS does not like it as their antiquated systems can't match up the 1040X filing with the part of the IRS that sent the notice.  That is not the taxpayers fault or responsibility.  I have been filing 1040X's for nearly 30 years from CP2000 notices and such and it is only in the last year or so that there have been problems due to the computer system disconnect and lack of IRS manpower for someone to actually read the amended return and look at the attachments.  Every amendment specifically states that the 1040X was initiated by a CP2000 or other notice (with a copy .pdf attached if e-filed or a copy stapled if paper filed) and the response back on the notice is that the taxpayer filed a 1040X to resolve the matter.   It is up to the IRS to sort it out after that.