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Florida concluded the first phase of a tumultuous recount of its midterm election on Thursday, with state officials ordering a manual recount in the hotly contested Senate race, while Ron DeSantis, a fiery conservative and enthusiastic ally of U.S. President Donald Trump, held his lead in the governor’s race.

Mr. DeSantis held a 33,683-vote lead over Andrew Gillum, the 39-year-old Democratic Mayor of Tallahassee, a margin of 0.41 percentage points – enough to avoid state officials ordering a manual recount.

Mr. Gillum made it clear that he would push to have all ballots – including some of those initially rejected because of mismatched signatures or other problems – counted before any election results were certified.

“A vote denied is justice denied – the State of Florida must count every legally cast vote,” he said in a statement. “As today’s unofficial reports and recent court proceedings make clear, there are tens of thousands of votes that have yet to be counted. We plan to do all we can to ensure that every voice is heard in this process.”

He added, “It is not over until every legally casted vote is counted.”

But Mr. DeSantis said the new results were “clear and unambiguous, just as they were on election night.”

Mr. Gillum had initially delivered an emotional concession speech to his supporters late on Election Day, then withdrew his concession as the vote margin narrowed and Democratic lawyers filed a flurry of lawsuits to allow additional ballots to be counted.

Meanwhile, state officials ordered a manual recount in the Senate race, where Florida Governor Rick Scott, a Republican, held a 12,603-vote lead over Senator Bill Nelson, the incumbent Democrat – a 0.15 percentage point margin.

Mr. Scott, who is leaving the governor’s office, had earlier calculated a slightly higher vote margin. Under state law, a manual recount is triggered in contests in which the margin is less than 0.25 of a percentage point.

In any case, he called on Mr. Nelson to concede.

“Last week, Florida voters elected me as their next U.S. senator and now the ballots have been counted twice,” Mr. Scott said in a statement. “Our state needs to move forward. We need to put this election behind us, and it is time for Bill Nelson to respect the will of the voters and graciously bring this process to an end, rather than proceed with yet another count of the votes – which will yield the same result, and bring more embarrassment to the state that we both love and have served.”

Mr. Nelson was said to be committed to fighting until all his legal options are exhausted, several people close to the three-term senator said.

His lawyer, Marc Elias, said the manual recount – which must be completed by Sunday – would finally provide the answers the Nelson campaign had sought. The count will not tally all votes cast, but will examine all ballots in which voters either cast two votes for one race, known as an overvote, or none, known as an undervote.

“We will be able to see whether there were markings on those ballots or not,” Mr. Elias said in a conference call.

The Associated Press said it would not call any of Florida’s races until the results were certified by state elections authorities. That is scheduled to happen on Nov. 20.

As of the 3 p.m. deadline for a machine recount of three close statewide contests, nearly all of Florida’s 67 counties – with the exception of Palm Beach and Hillsborough counties – had reported updated results. Broward County filed its results two minutes after 3 p.m., only to see them rejected for being late.

“Basically I just worked my ass off for nothing,” said Joseph D’Alessandro, the county’s election planning and development director. He said he had difficulty uploading the results because he was not familiar with the website.

In all three cases, initial vote results reported before the statewide machine recounts will stand.

But Broward County made the deadline only barely, and other counties ran into problems, raising some questions among some candidates about the reliability of the results.

“We have been the laughingstock of the world election after election,” Judge Mark Walker of the U.S. District Court in Tallahassee told lawyers battling over the recount in his courtroom on Thursday morning. “Yet we still chose not to fix it.”

The machine recount that began over the weekend ran into significant problems in Palm Beach County. Authorities there said the tabulation equipment came up short “a significant number” of ballots in the final Senate tally, making it impossible for the county to meet the Thursday deadline.

The initial phase of the recount was the subject of about a dozen lawsuits over which ballots would be counted and what deadlines would apply. A federal judge ruled early Thursday that voters whose mailed ballots were rejected because of mismatched signatures should be given a few days to rectify their ballots.

With Palm Beach County unable to produce a final tally in time, lawyers held a hearing in federal court on Thursday morning on a Democratic Party effort to get the recount deadlines extended. Justice Walker asked a question none of the lawyers seemed able to answer: Would it be legal to proceed with recount results that are missing one county?

“There is no constitutional right to have your vote counted a second time or a third time,” Mohammad Omar Jazil, a lawyer for the Florida Secretary of State, told the court.

Democratic lawyers filed a new lawsuit Thursday afternoon against Palm Beach County, seeking a hand recount of all ballots in the county “due to systematic machine failure during the machine count,” Mr. Nelson’s lawyer, Mr. Elias, said on Twitter.

The problem in Palm Beach County is with antiquated vote-counting machines that do not allow multiple races to be counted simultaneously. The county had put a priority on recounting the Senate race, which was listed first on the ballot.

One reason for Palm Beach’s delay was that its tabulation machines overheated earlier this week, creating the need to count nearly 200,000 votes again. An additional problem surfaced later, according to the Palm Beach County elections supervisor, Susan Bucher: After the mechanical failure was corrected and the machines were restarted, they apparently failed to tabulate entire boxes of votes – the totals now do not add up, Ms. Bucher said.

Ms. Bucher would not say exactly how many boxes of ballots were missing from the count.

“A little bit more than a dozen precincts lost substantial numbers,” she said.

Workers were having to look through count logs to see how many ballots are missing from each precinct, and try to figure out, based on the numbers of ballots in the box, which of them might have to be put through the machine again, she said.

Despite all the problems, most election workers in Palm Beach County did not show up for work until about 10 a.m. Thursday. Ms. Bucher defended her decision to let her exhausted staff go home at 9 p.m. to sleep and eat. A skilled team of three workers needed to be alert Thursday morning to try to solve the machine malfunctions, she said.

“You can’t just have anybody run this,” she said. “You can’t do this kind of work with no rest, you just can’t.”

Officials in Hillsborough County said they could not submit recount totals because the count had resulted in 846 fewer votes than originally counted. The office had experienced two power outages during the recount that may have led to the discrepancy, they said.

“Conducting a full recount in a constricted time period is extremely challenging,” the county’s supervisor of elections, Craig Latimer, said in a statement.

Separately, Justice Walker ruled early Thursday that Florida’s law that allows county election officials to reject vote-by-mail and provisional ballots because voters’ signatures do not match the ones on file threatens to unconstitutionally disenfranchise thousands of voters. His order gives voters whose ballots were invalidated by signature mismatches until 5 p.m. Saturday to resolve the problems with their ballots. The new deadline would apply to a certain number of the just over 4,000 voters who were notified late that their mail-in ballots had been rejected because of a signature mismatch. Those voters will now have until Saturday to confirm their identities.

There are dozens of reasons a signature mismatch may occur, even when the individual signing is in fact the voter,” the judge wrote. “What this case comes down to is that without procedural safeguards, the use of signature matching is not reasonable and may lead to unconstitutional disenfranchisement.”

Mr. Scott’s campaign said it was filing an immediate appeal. They emphasized that the ruling applies only to a small subset of people – it is not clear precisely how many – who had received late notifications about their rejected signatures.

“We are immediately appealing this baseless decision and we are confident we will prevail in the 11th Circuit,” a spokeswoman for the Scott campaign, Lauren Schenone, said in a statement.

Later in the day, however, the 11th U.S. Circuit Court of Appeals denied a Republican request to stay the order allowing voters additional time to verify their ballots.

Although the rejected ballots were split among party lines, with slightly more Democratic votes, they disproportionately affected young voters. Daniel Smith, an elections expert at the University of Florida, said 26 per cent of the ballots rejected for user error belonged to people under 30, even though young voters constituted only about 7 per cent of those who voted by mail.

Smith’s tabulations show the number of ballots rejected for signature or other user error problems at 10,000, more than double the preliminary figures the state provided to the federal court.

“It’s not like nobody could see this coming,” said Howard Simon, executive director of the American Civil Liberties Union of Florida, which this year commissioned Smith to conduct a study on various problems with mail-in voting.

The Scott campaign lost a separate legal bid in Broward County, where lawyers asked a court to order the county to stop counting ballots that had not been counted in time for Saturday’s initial deadline for vote results.

“We are very hopeful that any future attempts to stop the counting of timely ballots by lawful voters will take heed,” said Myrna Perez, a lawyer at the Brennan Center for Justice, which represented the League of Women Voters and Common Cause in successfully contesting that case.

Nelson filed another suit on Thursday, this one challenging the decision by an elections supervisor in hurricane-damaged Bay County to accept a handful of ballots that had been submitted by fax and e-mail.

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