Regiments carried individual flags. In a few cases a regiment carried the same flag for its entire career, but this was unusual. The 46th Alabama almost certainly lost its flag during the Vicksburg Campaign. When the five regiments assigned to the Alabama brigade under General Pettus reorganized, they received new flags. Prior to Vicksburg, regimental flags probably looked different but all modeled on the First National. Afterwards each of the regiments in this brigade would have received a flag almost identical to one another.

Here's the index of flags in the State of Alabama collection. You can ask on the Flags message board about the flag pattern, but be sure to mention which period interests you: before or after Vicksburg. Before the Vicksburg Campaign, this regiment served in east Tennessee, Kentucky (briefly) and middle Tennessee. Afterwards the 46th Alabama served with the Army of Tennessee, mainly in Georgia and Tennessee.

http://www.archives.alabama.gov/referenc/flags/intro.html