From a few years of experience, I've noticed that brown coloured permanent pen marks are the most easily erased. Conversely permanent blue marks can stain the film covering forever, if left on the chart too long and will not come off, even with a solvent, because the ink actually combines with the plastic.
Having said that, I've got a little cardboard box containing almost a gross of brown chinagraph pencil lead refills in my personal stash, so I don't use permanent marks very often these days.
I use mainly just track lines marking the chosen route, sometimes with miles to go leading to the turning points, if I've got time.