There is one other factor to consider; some records were simply not kept.

At the end of the war both paper and ink were in very short supply in the Confederacy. The Confederate army did a remarkable job of record keeping and I have found copy of reports of desertions, from very late in the war, written on scraps of plane paper with the lines and column headings hand written because no printed forms were available. But in the spring of 1865 some reports may have been reused for other things (like letters home) by writing on the back of the paper, and because the end of the war was obvious and Gen. E K Smith had left Shreveport, a general apathy probably set in and no records were kept.

One other item, when the war ended many of the CS government buildings and warehouses were looted by the Confederate soldiers (they had not been paid of week, etc.) and some records were probably destroyed in the looting. The looting got so bad that some CS army regiments, in Shreveport and other places, took it upon themselves to act as law enforcement until Union troop arrived.