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.
It is up to the preparer to help the client deal with IRS in the most efficient manner, which usually means following IRS instructions. You can file an amended return, which even if e-filed goes to one city and sits in one place for ten months before being worked. Or you can answer the CP-2000 notice, which is being worked in another city by an IRS employee with deadlines who is not trained to process 1040-X forms. Or you can mix and match, sending a 1040-X to the wrong address and figuring IRS deserves a square peg pounded into a round hole because your client forgot about a brokerage account.
