Hope this does not happen to anyone else, but I found a solution in case you find yourself in a similar situation.
I had completed a quilt for my soon-to-be-born grandson's baby shower and washed it with color catchers. But one of the fabrics faded in the wash in a most uneven fashion - it seemed as though the fabric was defective and did not hold the color consistantly.
So I found a Sharpie marker called Stained with brush tip that is designed for fabric and dabbed tiny little dots to fill in the missing color.
It looks soooo much better! Here is a picture of one of the faded parts and the "touched up" area to the right and a picture of the top before quilting and washing.
The design for the quilt came from this quilt a long website