You do not need to file an amended form 1099-Misc and you do not have to amend your tax return. You did the right thing by filing the 1099 form based on the payments you made to the subcontractor in the year you made the disbursements. It is up to the contractor to handle the receipts properly on his tax return. If the contractor files his tax return on an accrual basis, he would report his or her sales based on what was billed out during the year, as opposed to what was received. Although this may not coincide with what is reported on the form 1099-Misc, you should not complete the form 1099-Misc based on your contractor's method of accounting.
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