When the 1099k was first introduced, I received both a 1099k from my payment processor at the time and a 1099nec from one of the companies I contracted with.
Around September that year I received a nasty letter from the IRS accusing me of tax Fraud. I called the IRS and the operator was extremely rude accused me of tax fraud as I explained to her that the two different 1099s had duplicate income.
The end result was that I had to print out all invoices to that client and the related transaction history from the payment processor.
Hopefully the IRS has figured this out by now but I doubt it.
Edited: Since posting earlier today, I see the answer is to enter the difference as an expense labeled 1099 duplicate income.
