RALEIGH, N.C.—Josh Howard is playing with fire here in the heart of the old Confederacy, with a scholarly finding that could rewrite the history of the Civil War.

For more than a century, North Carolina has proudly claimed that it lost more soldiers than any other Southern state in the nation's bloodiest conflict. But after meticulously combing through military, hospital and cemetery records, the historian is finding the truth isn't so clear-cut.

Official military records compiled in 1866 counted 40,275 North Carolina soldiers who died in uniform. Though known to be faulty, those records have gone largely unchallenged. With most of his research done, Mr. Howard has confirmed only about 31,000 deaths. "It's a number we can defend with real documents," he says. He expects to confirm a few thousand more by the time he finishes this summer, but the final tally will most certainly fall short of the original count, he says.

Across the state border in Virginia, traditionally believed to have the fourth-highest number of war deaths in the Confederacy, librarian Edwin Ray has identified about 31,000 Virginia soldiers who died in the war—more than double the Old Dominion's once-accepted number of 14,794. And he still has more to add.

"It's going to be close," says Mr. Ray, a 55-year-old Air Force veteran who works at the Library of Virginia. "Josh and I are sure of that. It's going to come down to a very small number."