Warn your client to expect an IRS notice proposing SE tax on the "nonemployee compensation" -- probably income tax also, if the GS-3 clerk working the case doesn't spot the same number on Schedule E.  The payor might be willing to file amended MISC and amended NEC -- less likely, might be able.  

Attaching an explanation doesn't hurt.  At least it will be handy to respond to the IRS notice, 18 months later.  

IRS uses Artificial Stupidity to pick returns for audit.  One thing the program looks at is total positive income before deductions, so reporting the same income twice adds to the total and therefore the score.  Another thing it looks for is a high ratio of expenses to income on Schedule C -- 100% will earn you some points.  George's method might work, or it might push the score over the limit for winning an audit.