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Some facets disappear and reappear while navigating through the scene. This behavior may or may not be noticed when the 3D scene has been exported to a VRML file and viewed with a third-party software.
The large values of the X an Y coordinates of the geographic data in the 3D scene are causing a loss in Z-buffer resolution.
When the scene is exported to VRML, the surface coordinates are transformed to center on 0,0,0. This should prevent the Z-buffer resolution from being adversely affected.
Transform or project the data to have it located closer to the 0,0,0 origin. This should yield better results in the 3D scene.