The CS brass tried to discourage the wearing of Union blue for the entire war. One way to make use of captured uniforms was to dye them another color. This happened on numerous occasions not just in the valley. There are ancedotes available and you may check the on line ORs for mention of orders to dye or ditch.
Try to go here and do a search for dying uniforms or similar key words. Don't ask the question or you will get mauled for not doing a search first. You may have to join. http://www.authentic-campaigner.com/forum/index.php
Research projects are fun.