From the help for Add Spatial index:If you find it didn't automatically update, you can run both tools to remove and then add the spatial index.
I know that exist a tool Add Spatial index but I haven't found one that just update or recalculate my spatial index. Is there one?
By default, ArcGIS creates and maintains a spatial index for geodatabase feature classes. For a geodatabase feature class to not have a spatial index, you must explicitly remove it using the Remove_Spatial_Index tool
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