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Split Polygons based on Second Polygon Layer

MeKohler

Hi, I have a layer in which larger polygons contains smaller polygons, but the smaller polygons aren't included in the geometry of the larger polygons. I.e. no islands.

Using the intersect tool, I was able to identify these polygons, creating a new polygon layer.

Is there a way to use the intersect layer to split the original polygon layer. I don't want to erase these polygons, I just want them to have the correct internal boundaries. I tried the Geoprocessing Split Tool, but I didn't get the results I was looking for. It created separate layers for each There are a large number of polygons so I'm looking for a way to overlay the 2 layers.