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Now i don't understand you.

Anyway, my idea is...you got alpha chanell which isn't "solid". Alpha chanell is greyscale image. 0% black is 100% transparent, 100% black is 0% transparent. Everything between is more or less transparent. So idea is bring those bits who isn't 0% or 100% black to one or other side. You can choose method you want. You can copy/paste it in new layer and convert to Bitmap it and copy/paste back.

You can use Threshold to it. Which actually gives very good result and probably is better that my previous advice.

 So think of Alpha/mask as greyscale image and be creative. You can do to it everything you can do to a normal greyscale image.