I ran across this in a book I just purchased. Though the book contains very little about the Cherokee or the Civil War in Indian Territory, it does contain Slover's description of what appears to be the flag presented by Albert Pike to Col. John Drew, 1st Cherokee Mounted Rifles.
Note that Slover, "The Missionary", oddly refers to himself in the 3rd person. Slover was the first Southern Baptist Missionary in the Cherokee Nation and served in that capacity 1857-1862. The Southern Baptists did not bar slaveowners from their congregations as did the Northern Baptists (e.g., Evan Jones). The Keetoowah were hostile toward the Southern Baptists considering them "pro-slavery".
Slover, James Anderson; (edited by Barbara Cloud); Minister to the Cherokees: A Civil War Autobiography
The Missionary was a looker on on the day the treaty was returned from the Confederate Government at Richmond, Va., and the one thousand Indians were received as Confederate soldiers. He saw the white flag with a blue half moon sewed on it with a red star located just between the two horns of the moon. The red star represented the Cherokee Nation, the half moon represented the Confederacy.
The description of the "horns of the moon" seems to suggest this was a crescent moon instead of a "half moon".
…But there was doubtless an underground communication that reached Blunt on the return of the messenger, because the next day after the surgeon and the young lady escort left the Chief’s, the Treaty Regiment of Confederate soldiers which were in camp on the Prairie nearby mutinied. Their Colonel had to flee for his life with ninety of his men, and he lost his hat. The whole of the Regiment except the ninety raised a white flag with a red star in the center and marched in single file to Gen. Blunt’s headquarters.
Slover is describing the events in July 1862 during the 1st Indian Expedition when Union Capt. Greeno and Dr. Kirkpatrick met with Chief John Ross at Park Hill.
Slover repeatedly mentions "Gen. Blunt" and "Blunt's headquarters" but, of course, Col. Weer was the commander in the field and Blunt was in Kansas.
The term "Treaty Regiment" refers to Drew's Regiment created by the treaty with the Confederate States (not the Treaty Party led by Stand Watie). Drew and a few loyal Confederates fled to Ft Davis. It appears that the "blue moon" was removed by the Loyal Cherokee when they defected to the Union Army.
As a side note, it is a common error that Greeno escorted Chief Ross and family from Park Hill to the north. This is not the case. Chief Ross was arrested and paroled at his Park Hill mansion (Rose Cottage) where he remained for three more weeks.
Greeno 'captured' the officers of Drew's Regiment, including Lt. Col. Ross, and took them north where they and most of the regiment were enrolled in the 2nd and 3rd Indian Home Guard regiments.
In early August 1862, Col. Cloud went to Park Hill and escorted Chief Ross with his family and a few friends, along with the Cherokee Treasury, north to Kansas.