Did you iron the cloth after sketching before stitching? That would set the ink on my Frixxon washable pen.
Did you scrub the lines when washing it? I found I had to vigorously scrub the material together to get the ink to release on my Frixxon pen. In my case I was doing FMQ on an ivory background using black Frixxon ink. Anything that had any kind of heat near the pen took a lot longer and a lot of scrubbing to wash out. It did eventually all wash out, so don't give up hope yet. Just try to scrub it like crazy. You may have to patch your hand embroidery if the pen was near those applique, but that is easier than trashing the entire quilt!
Good luck!