Well, I was just at our bi-monthly reptile expo. So I brought the issue of the marker up with a vendor.
A breeder told me that there are serveral safe markers to use. They are Not like conventional paper markers but leave a latex-like-sheet or something that painlessly dries and flakes of in a few days. I see it used a lot with sexing baby dragons because they sell so fast at expositions that the vendors dont have time to sex them all during the show, so they put a red or blue dot on the tail for male and female.