TALLAHASSEE — The five-day sprint to run ballots in Florida through counting machines for a second time ended Thursday, with the state ordering a manual recount of results in the U.S. Senate race, where about 12,600 votes separated Democratic incumbent Bill Nelson from Republican Rick Scott, the state’s governor. No such measure was ordered in the governor’s race, where former Republican congressman Ron DeSantis held an edge over Democratic Tallahassee Mayor Andrew Gillum.

At least three counties did not submit new totals for the machine recount and are relying on counts from last week. Palm Beach County’s election supervisor said less than an hour before the 3 p.m. deadline that they would not finish the machine recount in any of three statewide races still in question and would move on to the manual recount at 4 p.m. In Broward County, results from the machine recount were received at 3:02 p.m. — two minutes past the deadline. And in Hillsborough County, officials said the number of votes after the recount was lower, but the margins in the races were the same, so they were sticking with the first unofficial returns.

In the governor’s race, DeSantis held a 0.41 percent lead over Gillum at the start of the recount, outside the 0.25 percent threshold for a hand recount. Gillum said in a statement that he would not concede.

Early Thursday, Judge Mark Walker of the U.S. District Court in Tallahassee ruled that at least 4,000 voters must be given two extra days to resolve issues with their signatures and have their ballots counted. The decision affects Floridians who cast mail-in or provisional ballots but whose signatures did not match records maintained by state officials. More than 4,000 ballots across 45 counties in Florida were rejected because of inconsistent signatures, he wrote in his opinion. In the other 22 counties, the number is unknown.

Nelson’s campaign filed a suit seeking a public list of all voters with mismatched signatures, while Scott’s campaign said it was appealing Walker’s decision. “We are confident we will prevail,” Scott campaign spokeswoman Lauren Schenone said in a statement.

While the ruling gives Nelson new hope for chipping away at his deficit, it falls short of the more sweeping decision his lawyers sought and is probably not enough to change the outcome of the race on its own.

Walker emphasized the court was not instructing county canvassing boards to “count every mismatched vote.” But he said the state’s process for curing ballots with irregular signatures had been applied improperly, robbing voters of the chance to make corrections before Nov. 5. State law requires canvassing boards to notify voters “immediately” if they determine a mail-in ballot contains a signature inconsistent with the one on file.

Palm Beach County Supervisor of Elections Susan Bucher holds up a tally sheet while speaking to members of the media at the Supervisor of Elections office after the deadline for a recount was reached Thursday in West Palm Beach, Florida.

It was unclear how many of the ballots rejected over signature issues would be subject to review. Walker said only that those voters who were “belatedly” notified their ballot was rejected would be given until 5 p.m. Saturday to fix any issues.

Marc Elias, Nelson’s lead recount attorney, praised the ruling. “We look forward to ensuring that those voters who cast lawful ballots have them counted,” he said in an email.

In his court decision, Walker stopped short of invalidating the signature-match requirement, concluding instead that the directive had been applied unlawfully because so many voters were given no chance to fix their rejected ballots and prove their identity. He also declined Nelson’s demand that all the mismatched ballots be counted “sight unseen,” as the judge put it.

Drawing an analogy to the rules governing football, Walker declined to throw out the regulation just because there had been a faulty call, observing, “Football fans may quibble about the substance of the rules, but no one quibbles that rules are necessary to play the game.”

Walker said the plaintiffs, the Florida Democratic Party and the Nelson campaign had established “irreparable injury” to the constitutional right of citizens “to cast their ballots and have them counted.” Specifically, Walker noted that while the deadline to submit a mail-in ballot was 7 p.m. Election Day, the deadline to “cure” a mismatched signature was 5 p.m. Monday, the day before – meaning those voters not notified or notified too late had no recourse.

There was similarly little recourse for provisional voters – those who cast special ballots subject to verification because they showed up in person on Election Day unable to verify their eligibility to vote.

Canvassing Board chair Judge Betsy Benson, left, and board member Judge Deborah Carpenter-Toye, right, show political lawyers one of the ballots that was damaged during the recount that will need to be duplicated and then recounted, at the Broward County Supervisor of Elections office on Wednesday.

There was new tension on another front, as Scott’s campaign manager called on Nelson to urge state Democrat Party Chair Terrie Rizzo to resign. The call came in the wake of a revelation that the Florida Department of State, which oversees elections, asked state law enforcement officials and federal prosecutors to investigate allegations that Democrats sent incorrect voting instructions to mail-in voters in four counties.

In another case, a Broward County judge ruled Thursday against Scott’s bid to exclude votes tallied there after Saturday’s initial counting deadline, saying he wasn’t going to approve it because there are other means to argue that some ballots shouldn’t be included.

Officials in Broward needed to duplicate fewer than 400 damaged ballots and run them back through a machine before announcing its new tally. The manual recount expected in the Senate race would begin at 7 a.m. Friday.

There will be 100 tables set up with two election workers, two campaign representatives and two party representatives at each, according to instructions distributed by election officials. Only the election workers are allowed to handle ballots, while wearing gloves.

The recount is scheduled for 11-hour days Friday and Saturday, with two 30-minute breaks each day. The deadline is noon Sunday.

“The table participant stays all day,” the instructions say. And that is not the only rule for volunteers working the recount: No phones at the tables. No pencils or pens. No food or beverages. Hands must be lotion- and oil-free in case of accidental contact with ballots. Activists for both parties quip that they are scouting for volunteers willing to go for hours without snacking or moisturizing.

The Senate race will determine the size of the Republican Party’s majority in 2019 and shape the power structure in the nation’s largest swing state. Together, the two sides have racked up at least 10 lawsuits trying to gain a legal advantage in the recount.

Scott’s campaign announced Thursday that it had raised more than $1.4 million for its recount efforts.

Reinhard reported from Lauderhill, Fla., Gardner reported from Fort Lauderdale, Fla., and Rozsa reported from in Palm Beach, Fla. Isaac Stanley-Becker contributed to this report.

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