IMO this is a systemic problem at the IRS.  While there are software worksheets, there are no IRS forms to report something that ends up being non-taxable.  I had a partially taxable one last year where I attached a free-form note explaining that $xx,xxx of education expenses were for Name SSN, leaving $y,yyy as taxable income reported on $wherever_they_moved_line_21.

The IRS does have some sort of document matching on these things so tell your client to expect a letter and call you ASAP when they get it.  I doubt attaching a note to the return will help (they really need to come up with a form for this!) but it makes it easier to resolve later.  I've been told by a manager in the AUR unit that all CP notices are reviewed by a human before being sent out.  Based on some of the CP notices I've seen, I personally find that hard to believe.

Rick