VPG and ute.no sell (or at least they sold) a Tendon Rope Marker. I have marked most my cams with it and after falling on nearly all of them, can happily state that the tendon rope marker doesn't seem to have a negative effect on nylon. Indeed, Black Diamonds QC Lab (link below) seem to suggest that even using a house hold tusj will probably have no effect on nylon (Link located below). Be warned that earlier testing done by the UIAA stated that there could be decreases in the strength of material up to 50%.
http://blackdiamondequipment.com/en/qc-lab-can-i-use-a-sharpie-to-mark-the-middle-of-my-rope.html
https://industri.vpg.no/Avdelinger/Industri/Diverse---industri/Kniver-og-multiverkt%C3%B8y/Tendon-Rope-Marker-121873-p0000135030