How did the Confederacy come to be symbolized in the flag that roils American politics to this day?

In their quest to symbolize their foundational values of freedom for whites and slavery for blacks, Confederate leaders spent two years trying out and rejecting a variety of emblems. Only in March 1863, well into the Civil War, did they finally adopt the pattern that is so familiar today, after initially rejecting it four to one.

This rarely discussed history emerges from the work of Raphael P. Thian (1830-1911), who was in charge of transcribing Confederate records from the seized rebel archives in Richmond, Va., after the Confederacy’s surrender. Initially, the federal government thought the documents might yield proof of complicity by Jefferson Davis, the Confederate president, in the assassination of President Abraham Lincoln. No such evidence emerged, and the federal government lost interest.

Mr. Thian did not.

I came across Mr. Thian’s work and the history two years ago in the Museum of the Confederacy (recently renamed the American Civil War Museum) after learning that my uncle, an African-American man, in an act of radical empathy, had joined the Sons of the Confederate Veterans on the strength of his enslaved ancestor, who had been a cook and a river guide in the Confederate Army of Northern Virginia.