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Is there a way to incorporate an etch factor into the gerber file before I export it to dwg/dxf? An etch factor is basically offsetting the outside border by half the Cu thickness. Basically making the outside border larger all around by say 0.005” for example. The problem comes in though when there is an opening within the pattern as that now has to shrink by 0.005” instead.

To add 'etch-factor' to gerber files, you may want to try the feature called "Grow / Shrink", located in the menu:  Fabrication. / Grow / Shrink...