Solved! Go to Solution.
Try invalidating the spatial index.
Here is another doc that goes into more detail on working with indexes
IPolygon poly = (IPolygon)myAxMap.TrackPolygon(); poly.SpatialReference = mySpatialReference; IPointCollection p = poly as IPointCollection; IGeometry geometry = p as IGeometry; geometry.SpatialReference = mySpatialReference; ((IZaware)geometry).ZAware = false; string shapeFileURL = CreateShapeFile(p , LayerName); //Where this generates a valid shp file and returns the full file path AddLayer(shapeFileURL); //Where this creates the ILayer , sets the layer effects and adds it to a group in myTocControl ((ISpatialIndex)poly).Invaldiate();