I think it's the disappearing pens which can come back to haunt you. The pencils which supposedly wash out either wash out or fail to do so; I don't think they wash out and then come back. (But then the ones which don't turn out to wash out after all are quite enough trouble already, thank you.)
There are a number of marking tools out there, and none are perfect for everyone. Most of us are still struggling to find the perfect marker. Be aware that many markers will be set permanently by ironing, and some will rub off through friction by the time you've finished the quilt (especially with hand-quilting), and some might do odd things such as leave smudges (some types of chalk, soft graphite pencils). If you're not sure, just ask here, there will be people with years of experience with that particular marker who can tell you what it gets up to.