I had the same issue. I quilted a top that my Mom had made and marked and then stored for over 30 years. All the pencil marks were in the white areas. I quilted it up and then washed it, and they all were gone. This was a quilt for a sister and I knew she'd be happy to have it even if it did have light pencil marks - much better than not having it at all.
My Mom had planned on hand quilting it, and I did it on the LA.