What I've been using recently for embroidering is a fine brown permanent Pigma pen. It's amazing how it is totally covered with your stitching, or blends in so well, and you can get such a fine line rather than the heavier lines the disappearing pens make. Not sure whether I first read that on one of my Crabapple Hill patterns or where, but it works great, and the ladies at the LQS all use it now too.
Hope your carbon comes off for you.