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Typically the scratch is below the surface of the hone. As long as the edge isn't catching on it, it should be fine.

If you can feel it while honing, there's a problem.!! Lap it flat

Might be the diamond plate. Try 600 or 1000 wet dry paper, on a flat surface.

Lap it if it bothers you. I've done that a few times myself, with Thurigan and Coties.

I typically use slurry. By doing so, it removes the light scratches left from previous honing.