In order to file an amended return, he would have to be issued a corrected 1099-MISC first, for the year he was overpaid and for which he would be amending for. If you issue a corrected 1099-MISC, then you too will have to file amended returns.
Otherwise, if they just give back the overpaid amount in 2016 with no corrected 1099-MISC, then that's considered a 2016 transaction of which the payer can deduct from their 2016 income, and the receiver has to claim as 2016 taxable income. This could change the tax bracket of one or both parties involved in the transaction, and could also change the qualifications for both or either party, for tax breaks they would otherwise qualify for.
