That may be a technically correct way to handle this - if they sent you a 1099-MISC and shouldn't have, a corrected 1096 (Annual Summary and Transmittal of U.S. Information Returns) would not include a 1099-MISC for you. 

Unfortunately that doesn't give you anything to indicate you shouldn't have received one in the first place.

If you never received the payment reported to you on a Form 1099-MISC, do not report it on your tax return.

Keep a record (time, date, names) of your call to the employer and a summary of what they told you.

(If the amount reported is large, you should follow up the phone call by sending a written summary of the conversation to the company Send the letter with proof of mailing and proof of delivery.)

Should the IRS contact you for an explanation of why you did not report it, you can provide them with the information you have that proves it was an invalid 1099-MISC.