As a employer, how do I file an amended 1099 to IRS?
All you have to do is to mail Form 1096-Annual Transmittal Letter to the appropriate IRS Address as shown on Form 1096, (the mailing address is based upon your State of business).
When you mail Form 1096, include the amended or corrected 1099-Misc and check mark the Box that indicates "Corrected". This is shown on the upper side of the Form 1099-Misc.
The corrected 1099-Misc is all you have to include with Form 1096 and since it includes the check mark X against the "Corrected" box, this will tell the IRS that you are including an Amended 1099-Misc Form.
There is no check mark required on 1099-Misc Form.