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Lapping and flattening should take out any gouges that u may make. But of course the softer the stone the more likely the gouges can happen. But as long as you lap them smooth this would be no...

You can use both sides if you like one for knives and one for razors. But I don't see the point of doing so. It could be because of my inexperience but I would not see it mattering as long as you are...