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When you take the "extra" two layers of tape off, you'll be changing the bevel angle. So your bevel-setting stone will be removing metal where the side of the blade meets the bevel. And you'll...

Depending on how bad the warp is, you may or may not be able to "correct" it by honing.

You can also hone the edge, and keep the warp. It won't degrade the shave. The honing will involve both...