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I use geoprocessing with large polygon datasets.

I use Multipart_to_Singelpart and Repair_Geometry to remove all invalid geometries, prior using the tools like Union or Intersect. Regardless the correct geometries in the input data the result will contain invalid geometries. So, the invalid geometries appear during geoprocessing with ArcGIS.

These invalid geometries hamper further processing (ArcGIS freezes), so I desperately put a Multipart_to_Singelpart and Repair_Geometry in my script after every step of geoprocessing.

But is there a best practise or setting to avoid or reduce invalid geometries when geoprocessing in ArcGIS?

Using a projected CS (EPSG:4647) with ArcGIS 10.2.2 and ArcGIS 10.6

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    What kind of input data do you have? I have never experienced invalid outputs from Union or Intersect if the inputs are valid. Do you use delete_null='KEEP_NULL'? – BERA Jan 28 '19 at 12:54
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    I've been using Union and Intersect for 30+ years, and I've never generated an invalid geometry either. Please provide more details on: The version of ArcGIS in use, the coordinate system of the data, the spatial reference parameters, and the tolerance parameters utilized. This is probably a topic for Tech Support. – Vince Jan 28 '19 at 13:01
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    I, too, often get invalid geometries resulting from operations on "repaired" inputs. It occurs with projected coordinate systems, with coarse, fine, and default tolerances, and after deleting null geometries. It's more likely with denser vertices. In some of my processing, I have to run geometry repairs after every operation. – Tom Feb 5 '19 at 18:36