Complaints at dozens of polling sites for yesterday's primary have sparked separate investigations by the City Comptroller and the State Attorney General. But, we have uncovered another shocking fact — some New Yorkers who thought they were casting a ballot won't have their vote counted at all. Our Courtney Gross has this exclusive report.

For years, voters have feared that when they fill out a paper affidavit ballot at the polls, their vote won't count.

"Yeah it does concern me," said Shirley from Bedford-Stuyvesant. "But I did vote."

But in some cases, that vote is never counted at all.

"It includes about 70,000 voters who are archived," said Michael Ryan, executive director of the New York City Board of Elections. "Now if those folks showed up and they filled out an affidavit ballot, their vote won't count, but their registration will be revived."

The investigation surrounding the city Board of Elections handling of Tuesday's presidential primary has ballooned in just 24 hours. Not only is the city comptroller looking into it, but so is the state attorney general.

But as that investigation snowballs, NY1 has learned some of the votes cast by affidavit ballots on Tuesday may never be counted at all.

We found out an entire pool of voters is being punished by the board for not participating in several elections in a row.

Board officials call them "archived voters." In Brooklyn, as of Wednesday, there were 70,000 names on that list.

You become an "archived voter" if the board sends you an election notice but it is unable to be delivered. You are then archived if you sit out the next two federal elections.

Once on that list, if you show up at the polls and fill out an affidavit ballot, that ballot will not count. It will only reactivate your voter registration.

"We send you a notice in the mail saying 'Hey, we are going to cancel your voter registration if you don't respond back to us,'" Ryan explained. "And only those individuals who did not respond back to us and only those individuals who did not respond to our intent to cancel notice were archived."

This revelation is piling on an array of other complaints about Tuesday's primary, including New Yorkers who say they were missing from the voter rolls.

"My name wasn't on the ballot and they told me that the next time it would be and it wasn't," said Shirley. "So I had to do affidavit once again."

Despite all of this, the Board of Elections is giving themselves a vote of approval.

"This was a success story," Ryan said.