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I will try today again, and smooth the stone for a few mins with the 2k. To be honest the stone wasn't totally smooth while honing, I had a feeling like there are a few small particles here and...

Lapped the 12k with the atoma= the stone works very fast, the surface is a bit rough, cratches on the bevel.
Atoma lapping, smoothing with the 2k= surface is smooth, stone works really nice,...

I will try to smooth it out with my 2k, but won't grit get embedded in the 12k? Or if I rub them together with a lot of water and wash them afterwards than I will be fine?

I have the same exact problem with my newly purchased pro 12k, lapped with a new Atoma 400. The 2k is fine, the 5k is fine, the 12k scratches the bevel like hell, and is much worse in honing feel...