N.Y. Comp. Codes R. & Regs. tit. 9 § 6211.3
At the end of each day of early voting, those ballots which were not scanned because a scanner was not available or because the ballot was abandoned at the ballot scanner, shall, if a scanner is then available, be scanned by the election inspectors as provided for by Election Law § 9-110. A ny ballots that are unscannable because it is rejected by the scanner or because of an overvote or wholly blank vote warning provided by the ballot scanner, shall be secured in the manner applicable to voted ballots on election day and shall remain unexamined until the time of canvass on the day of the election, at which time they shall be examined as provided for in Election Law § 9-110 and duly canvassed. Such ballots shall be reconciled as required by the procedures of the state board and must be held inviolate until the time of canvass on election day under tamper evident seal and lock and key.
N.Y. Comp. Codes R. & Regs. Tit. 9 § 6211.3