I suspect these are two different individuals.

...

J. D. Baker, Private, Company I, Confederate Regiment Cavalry,*, enlisted December 27, 1862 at Santa Rosa, Florida by Capt. Amos for the war, recorded absent without leave since August 12, 1863, next recorded present December 31, 1863 and lastly June 30, 1864, no further records

Note, there are no subsequent company muster rolls surviving in the records

* This company was formerly Company D, 3rd Battalion Florida, Cavalry. It subsequently became Company I, 15th Regiment Confederate Cavalry (also known as 1st Regiment Alabama and Florida Cavalry)

M258: Compiled Service Records of Confederate Soldiers Who Served in Organizations Raised Directly by the Confederate Government.

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James Baker, Private, Company A, Hardie's Battalion of Cavalry, Alabama Reserves, enlisted April 15, 186_ at Talladega by Maj. Hardie for the war, his name appears on a muster-in roll of Company A, dated October 14, 1864 at Talladega, Ala., his presence, not stated, description: age 46, black eyes, black hair, dark complexion, 5' 8", resident of Talladega, Ala., no further records

Company record of event: This company was organized in May, 1863 for local defense. . . There is but one man in this Company between the ages of 18 & 45. He is a blacksmith . . . This company was mustered . . . the 15th April, 1864

M311: Compiled Service Records of Confederate Soldiers Who Served in Organizations from the State of Alabama