I love my F&P mechanical pencil. But I find the markings rub out very easily. I had marked the center of a quilt I am handquilting and by the time I got done with my first hoopful of quilting all my other markings had rubbed off! So now I use it to mark as I go, it was a hard lesson learned. Maybe because so much of the quilt rubs against itself when handquilting with a lap hoop you will not have the same problem with machine quilting. I suspect it will also stay better if loaded on a rack.
I don't know if ironing it will heat set your marks. You may wish to try it on a piece of scrap fabric if you have any left.