File Form 8824 and keep the 1099-S in your file. It's not necessary to be concerned with it when you complete your 1031 exchange. As indicated by tagteam a simple letter of explanation can be completed if the IRS does inquire. However unlikely since your return will have the Form 8824 with your return showing the 1031 like kind exchange. There is no need to be nervous.
@Em1
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