Should sharpening nicked knives with whetstones leave the nicks in the blade? This question is somewhat similar to How to sharpen knife with chunk missing?, but the knives I have are not ruined like the one in that question, and I doubt the answer here would be to just throw away the knives as in that question.

I have three different Classic Global knives – a G2, a G5, and a GSF22 – which are all somewhere between eight and ten years old. None of them have ever been sharpened before. Especially the G5 and the GSF22 have been frequently used, and the blades are showing the effects of that, so I’ve bought an MS5 ceramic whetstone to sharpen them.

I’m a complete novice when it comes to sharpening knives, especially with whetstones, so I did the usual thing first: watched some YouTube videos (Global have one themselves which was very instructional) and read up on it on the Internet.

The M5-OM whetstone I have is 1000 grit, which I realise is probably not really coarse enough to get efficiently rid of nicks very efficiently, but I didn’t feel like splurging on more than one whetstone to begin with, so I got the medium one to start with.

I’ve just sharpened all three knives now, and I admit the results are a bit underwhelming to me. The knives are decidedly sharper than they were before, but all the little nicks and chips in the blades that have developed over the years are still there – some of them actually look bigger now than they were before, which was rather the opposite of what I wanted to achieve.

For comparison, here are two superimposed images of the blade of the GSF22 before (top) and after (bottom) sharpening (click for full size to see the nicks better):



None of the nicks you see there are very big to begin with (the blade is 11 cm in total), but I would have thought sharpening the knife would at least have reduced them, taking material off the edge of the blade, but not where it’s nicked.

With this level of nicking, is it normal that sharpening the blade does not seem to affect the nick? Or does this level of nicking simply require a coarser grit than 1000 to even start getting rid of the nicks at all? Or is it evident from the photo that I did something very wrong when sharpening (over- or undersharpening, wrong angle, etc.), which may have exacerbated the nicks rather than getting rid of them?
You are indeed supposed to remove so much material from the blade that the nicks disappear completely. You'll have to lose what's probably a least a milimeter of the blade's width. 

For that, the 1000er grit is indeed too fine. Go for something much coarser, and use finer grits for finishing. With the stone you're using, you'll have to spend days to get so much steel ground away. Something in the 150-300 range will do nicely for the task you have.