I have offset the value of a 1099 received several times. I have not heard anything about it. Just enter an opposite value where the 1099 lands and add "see statement" and then include a short statement about your reasoning for questioning the value. The key is to get past the automated computer matching -- you have to report the amount that matches the 1099; just reduce it via a separate line item.
I believe schedule 1, part 1 line 8z is where your 1099 would land this year, and schedule 1, part 2, line 24z is where you can put your offsetting reduction in value. Consult a tax advisor, blah