I have just made my first solo attempt at sharpening my knives. Now while all my new knives are sharper than out of the box and my wrist is sans hair at the moment I have also left a lot of scratches on my knives. I'm using a Naniwa chosera 400 and a 1000 for now and am looking at something in the 5000/6000 range soon. What i want to know is down the track will it be possible for me to get these scratches out once I can sharpen without scratching them. And also is ther any chance that I can scratch through the cladding on my hiro AS?
Lots of sharpening scratches are a big part of learning to sharpen. And yes, once you are confident enough that you can sharpen without scratching up the sides of your knives, then it is possible to refinish knives to get rid of scratches. Some people use a progression of wet/dry sandpaper, I've had good results with 3m micromesh pads.
With your hiro as you will find that the cladding, being significantly softer than the core steel, will scratch very easily. It actually aids in sharpening ease, because when it is time to thin a san mai knife, the cladding is easier to remove than harder steel. I'm not sure what you mean by 'scratch through the cladding'. You're unlikely to expose the core steel above the cladding line, but if you did, it wouldn't be the end of the world.
Well done in your first sharpening session. If you're comfortably removing arm hair at 1000 grit, that is a great start!
The bad news: yes, you can remove the scratches with various grits of sandpaper. The scratches will be replaced by a much finer and even pattern of scratches. You will have to work on the entire face to get an even result. In fact, on both faces. By the way, with a very polished blade food will stick easier.
With carbon blades you don't have to worry about scratches: the patina will hide them.
The good news is about the Hiromoto: by no means you will get through your clad. The soft clad steel scratches easily but is not easily abraded, as you will notice with thinning. The cladding is relatively thick. Look at the spine: you may see three steel layers. In the center the core steel, about .5mm thick, and the outside cladding, .75mm each.
As the clad steel is so soft, scratches are just as easily removed as they do appear.