Well, I promised to report back, and here it is
Well, I've been working with a single unbranded CD-R with thick circular sharpie marks along the inner and outer parts of the CD-R. The postion of the sharpie marks was chosen so that I could easily spot it when I scaned the CD.
I have only been working with the CD-R since March 6th, but since then there has been no degridation, at all. Now I realize that it is really too soon to tell, so I did a little more testing on other CD-Rs.
I have a sort of pack rat like nature when it comes to CD-Rs. I try to keep every CD-R/W I've ever burned, even if they become partially, or completely unreadable... I know it's weird, but it has come in handy over the years on more then 1 occasion
I have been going through, and re-scanning all (yes *ALL*) of my CD-Rs recently, in my efforts to beta-test some new scanning software (k-probe by Karr Wang of LiteON IT), and I have been paying special attention to all the CD-Rs marked with sharpies, especially the REALLY old ones.
So far I have this to say: I can't find any proof that marking a CD-R with sharpies leads to quicker degridation of the media. I have some CD-Rs that were marked with sharpies, and in some cases MUCH WORSE markers, that have survived over 5 years without any problems, and are still in quite good condition (which is really impressive considering what some of them have been through!).
The one thing I should point out, is that all of my older CD-Rs were branded, most of them were Memorex, Maxell, and BASF (if you're curious). So I will continue my testing of the unbranded CD-R, in the hopes of coming to some conclusion of the effects of sharpies on a less protected media surface.
I hope this clears things up a little for people. I know I breathed a major sigh of relief!