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.