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Those anomalies (assuming they are at the shaving edge) will no long exist

If your hone is removing ink from every part of the bevel evenly, then the anomalies are not getting in the way of the...

You should keep honing with the stroke that passed the marker test until the problem is corrected :)

tape if you wish, it will speed things up, but it won't correct any fundamental flaw

I think only one bevel is sharp. use the marker test on both bevels and doublecheck your stroke