Hello again,
Yes, I am quite sure most militia uniforms dissappeared soon after active campaigning began in the war. Most militia companies had very distinct and different types of uniforms. Some, while looking good in a parade in the town square, had to be most uncomfortable on the march and campaign. That is why within no time they all had a generic uniform of shell jackets and pants. Some were issued frock coats too later. The 1st Alabama Vols was issued in 1862 blue-jean frock coats uniforms.

Have you ever read the articles by the "Military Company of Historians" on Central C.S. Government Issue Uniforms? Very informative. I think I have it copied in my files if you are interested. Let me know and I will e-mail it to you. I think it was a two part article. The C.S. Government actually had a good system and were producing good uniforms by mid war but the problem was getting them to the frontline troops.
Later,
Dave