It's not removable, that why the word "permanent" is on the markers.

I haven't seen it cause damage to the PCBs. The only thing you might do is slip and make a mark on the VFD glass or on the IR window where you didn't mean to. Or perhaps you might mark the glass in such a way that it blocks your view at a steep parallax angle. But otherwise it's not going to hurt anything I don't think. And watch that fill nipple on the VFD...