Your quilt is absolutely stunning, and after all the work that went into it I can see that you'd want perfection when it comes to the marking lines. I would too!
Have you tried using a fabric eraser? I'm also reading posts about using kerosene or lighter fluid on the yellow chalk.
Here's a funny thing I've discovered along that same vein: I found the very best cleaner for my kitchen stove grease and countertops is...Orange Glo furniture polish! Works like a charm and it actually dissolves the grease immediately, then wipe clean with a paper towel or dry cloth, so maybe they do have the right idea in using the kerosene or lighter fluid.
Not sure if this will help but there are several suggestions here that also sound promising.
http://sewing.patternreview.com/Sewi...ns/topic/51268