In modeller, load the object. Select the first layer you want to combine, making sure you're in Polygon mode with nothing selected press 'x' to cut all the polys. Select your second layer and press 'v' to paste the cut polys in.
If you need to then physically get rid of points/polys that share the same space, you can then use combinations of 'm' to merge points, or 'I' to unify polygons.
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