Conn. Agencies Regs. § 9-242a-26
After the polls close, the ballot clerks shall complete a ballot log summary prescribed by the Secretary of the State. They shall record on a form prescribed by the Secretary of the State the number of ballot packages received, the number of ballot packages remaining unopened after the polls close and the number of spoiled ballots, challenged ballots and ballots in the auxiliary bin after the voting tabulator was locked against further voting. If absentee ballots are counted in the polling place, the Secretary of the State shall prescribe how absentee ballots are accounted for. The ballot clerks shall place all spoiled ballots in a depository envelope marked "spoiled ballots", seal it with non-reusable tape and deliver it to the moderator for return to the municipal clerk. The ballot clerks shall secure all ballots which are not issued to electors and deliver them to the moderator for return to the registrars of voters. The registrars of voters shall store absentee ballots in a secure location for 14 days after which the ballots shall be given to the municipal clerk for the remaining storage period. All unused printed marksense ballots shall be retained by the municipal clerk in the manner and for the period prescribed by law for the retention of unused absentee ballots and then shall be destroyed.
Conn. Agencies Regs. § 9-242a-26