I ordered my T.E.C. Sharpie from these guys cause I couldn' find one locally. Arrived pretty quick and none of my ropes (nor my friends who used the marker) have yet to break in half. allenap.stores.yahoo.net/shtpema.html
A Sharpie or any other marker not specifically approved by rope manufacturers should not be used because of possible chemical interactions. The problem is that even if for example some type of Sharpie doesn't (or didn't) cause any problem there is no way to know if the formulation of the ink changes.
Rope manufacturers sell special markes which are compatible with the rope material.
Overall though polyamide is quite well resitant some chemicals like especially acids and bases can severely degrade fiber performance and the nasty thing about it is that it cannot necessarily been checked visually (and no one performs destructive testing excepted the manufacturers). UV has some influence but it's nothing compared to acids and bases.
Depending on how a rope is used its middle can be marked using a small piece of good quality heat shrink tubing (the one without hotmelt, for example Raychem RNF-3000), it's also very convenient to mark ends, for example using transparent heat shrink tubing to cover a non-adhesive label with the rope data and ID. Just make sure to not overheat it. If done correctly the rope is not damaged at all by the heat.
i have stitched floss/thread into the midpoint of my last several ropes and it has worked really well. i use about 4 or 6 strands, and weave it into the sheath in a spiral around the rope. the pitch of the spiral is approximately a 1/4", and i do it for a length of 2 to 3 inches. it lasts forever and you can feel it in the dark. i haven't seen any adverse wear or anything in the sheath.