I agree with DanMaloon… Don’t worry about it. I don’t think it hurts the value or the functionality of the knife. I have a hard time believing that you went that far past the original profile if you were watching the sharpie marking. It’s possible that there already was a little bit of recurve in the edge from the factory or a section of thin primary bevel along the dip. I looked at a web site where a fellow has a collection of them and there’s some variability in the bevels near the heel – simply because there’s variability in the thickness of the grind at that point.
There’s a picture of a sister of your knife at http://www.thetruthaboutknives.com/2013/07/the-united-colors-of-the-kershaw-skyline/ Serial number 399. Looks like you have #325? out of 500.
If it was mine, I simply spend a little more time stoning near the heel with each re-sharpening. If you use the knife enough, eventually you’ll straighten it out.