Well whatever you do, you need to ensure that geometry instance bounding boxes enclose all their vertices. Mesh instance nodes will calculate AABBs automatically for their normally transformed meshes but if you displace vertices in shaders they may go far out of those bounding boxes and the engine has no way of tracking how much the vertex shader displaced the vertices. When the bounding box goes out of the camera viewing volume, the object will be culled from the rendering pipeline, even if its displaced vertices are in the camera view. So check and maintain proper bounding boxes at all times, whether you’re using nodes and shaders, or the rendering server.
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