Coleman led Franken in election night returns and held a 188-vote lead before the board decided to review challenged ballots. However, both sides acknowledged that the lead could flip a few times before the long recount ends.
About 5,000 challenges were withdrawn after election officials asked that both camps pull back on unnecessary or frivolous claims in the interest of a faster recount.
The five-member Minnesota State Canvassing Board denied Coleman's proposal to reject 150 duplicate ballots that weren't run through a ballot machine and couldn't be matched to their originals, the Minnesota Star Tribune reported.
Board members ruled duplicates should be resolved by "another forum," yet to be determined, as they focused on ballots where there "are questions about the intent of the voters who cast them," according to the Star Tribune.
Minnesota Secretary of State Mark Ritchie said Thursday the board's goal of finishing the recount by Friday would not be met, the Washington Post reported.
"The only real concern is accuracy and transparency," he said. "Our job is to make sure we are absolutely certain how Minnesotans voted."
Franken's 250-vote lead over Coleman marks the Democrat's first lead since the disputed recount began, but Coleman's spokesman Mark Drake said numbers are expected to change as the vote counting continues.
"Because of procedural reasons regarding the way the process has been playing out this week, you will likely see the numbers continue to flip flop around and go upside down as a good-sized chunk of withdrawn challenges from the Franken campaign have not yet been awarded back into Norm Colman's column," he said, according to TheHill.com.
The recount's final result will be delayed by the outstanding issue of which rejected ballots will end up being counted.
More than 12,000 ballots that were originally rejected must be sorted through to determine which should be counted. Officials estimate more than 1,000 will be recounted, the Washington Post reported.
Also delaying the final decision will be the consideration of absentee ballots, which must be accounted for before Dec. 31.
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