Years ago the UIAA published a warning (and I even remember it being written up in one of the climbing mags) that using a Sharpie to mark your rope probably isn't a good idea. Here's the relevant excerpt:

Tests done by the UIAA Safety Commission and some rope manufacturers have shown that marking ropes with liquids such as those provided by felt-tipped pens can damage them; even with those markers, sold specifically for marking ropes. The test results have shown a decrease of up to 50% of the rope strength, more correctly: of the energy absorption capacity of the rope (expressed by the number of falls in the standard test method in accordance with the UIAA Standard101).Therefore the UIAA Safety Commission warns against marking a rope with any substance that has not been specifically approved by the rope manufacturer of that rope.Personally I questioned the applicability of these tests in real-world scenarios. The UIAA test is consistent and an industry standard for sure, but it's also extreme. Their test imposes a violent high-impact (fall factor 1.78 with a static belay) on the same section (in the above mentioned case, on the middle mark) of a rope, repeatedly, until it breaks. Not very realistic in everyday use. Think about that for a second: to have the middle of your 60-meter rope be the point where the rope is loaded during a fall, then you would have to be taking a HUGE 60-meter whipper—not very common.

At Black Diamond, we don't make ropes, and though we do have a drop tower, we don't have the ability to perform official UIAA drop tests. However, I'm a curious guy, so I had my crack crew of engineers grab a few cords, mark them up with a Sharpie, and pull them in the tensile tester. As expected, the ropes always broke at the knot—the Sharpie's middle mark seemingly having no effect on the strength of the cord during this test.