N.Y. Elec. Law § 9-106
After the polls of the election are closed and before any boxes or envelopes containing voted ballots are opened, the clerks, or if there be no clerks, two inspectors representing different parties designated by the chair, shall account for all of the paper ballots furnished to the election district or poll site. On a reconciliation form supplied by the board of elections, they shall count, verify and record on such form the number of unused ballots, the number of ballots spoiled before delivery to voters in the poll site, the number of ballots spoiled and returned by voters and the number of affidavit ballots cast. These numbers shall be added to the number of ballots cast as recorded by the public counter number appearing on the ballot scanner screen(s) or results tape(s). The sum shall be recorded on the ballot reconciliation form. This resulting number shall be deducted from the number of ballots originally delivered to the election district or poll site, and the remainder number shall be determined to be the number of ballots secured in the emergency ballot box(es) or other secure storage container(s) provided by the board of elections. This remainder number shall be recorded on the ballot reconciliation form. If such remainder number is zero and there are no ballots in the emergency ballot box(es) or other such secure container(s), inspectors shall initiate the ballot scanners' close the polls mechanism and produce results tapes. The clerks or inspectors shall then separate, label and place each type of ballot in the box or container provided by the board of elections, and securely lock or seal each such box or container and record such seal number on the ballot reconciliation form. They shall then sign such reconciliation form. If such remainder number is not zero or there are unscanned voted election day ballots in the emergency ballot box(es) or other such secure container(s), the inspectors or clerks shall proceed with the process provided for in section 9-108 and 9-110 of this title. Upon completion of such process, the clerks or inspectors shall then separate, label and place each type of ballot in the box(es) or container(s) provided by the board of elections, and securely lock or seal each such box(es) or container(s). They shall then sign such amended reconciliation form.
N.Y. Elec. Law § 9-106