How to stop a forming tool from removing existing holes?

I am trying to represent an emboss across a plate.  In the path of the emboss are holes which I would like to now conform to the emboss.  However, the forming tool removes any existing holes that it is forming around which doesn't make any sense because the holes would be punched first before forming it.  Is there a way to do this without introducing the holes in the forming tool itself?  It would be great to bring in a form to emboss a linear pattern of holes.

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