You need to confirm beyond all doubt, what box that income was reported in on the 1099-MISC. If it was reported in box 7 of that form, then it's self-employment income. Period. If it's reported in box 3 of the 1099-MISC, then you have a provable claim that it's not self-employment.
If the income was reported in box 7 of the 1099-MISC, then that gets transferred from the SCH C to line 57 of the 1040.
If the income was reported in box 3 of the 1099-MISC, then it gets reported on line 57 of the 1040 "UNLESS" an exception applies (and there are many exceptions.) In the case of an exception, it gets reported on line 21.
If necessary, contact the issuer of that 1099-MISC and see if they can issue you a copy. Also be aware that you have a time limit to challenge this, as indicated in the letter you received from the IRS. So don't waste time. Once the deadline to challenge their findings has past, you have no recourse.
