Thanks for your suggestions Michael. I could not regenerate it with BoltGen because it's only creating standard sized internal threads, you can't define length.

However I did some modifications and got rid of those edges.

In the future, some tool which removes unnecessary lines would be helpful for such occations, don't you think? I attached a file. There's a solid box and there are some intersecting lines on the box which contributes nothing to the shape definition. A tool should find those lines/points and remove them and rebuild the shape.