The letter your received is outside the normal tax return processing, and is usually handled by an individual agent at the IRS. Thus, different letters even on the same subject may have somewhat different instructions.
In your case, just read the letter very carefully and do whatever the letter told you to do, and don't worry about what other letters might have said. We have to assume that if your agent had wanted the 1040, he/she would have asked you for it.
