Yikes! I use pens to trace on the back of fabric (like if I'm using a template), and today I used one to make tiny little dots to mark so my quilted triangles would be even - but I made just a dot where each point should be and kept them on the other quilted threads so it wouldn't show up.
So sorry about the ink not coming out - it's such a lovely quilt. Hopefully some of the suggestions offered here will work!