So there is this cool video from epic featuring instanced meshes. Canon Man Tutorial: Hierarchical Instanced Static Meshes | Live Training | Unreal Engine - YouTube . It basically says that instead of deleting the x index in the hierachy. it gets replaced by the last index of it and thats going to be removed. so everytime you remove an index of it, the last index will be moved there. thats what ruined the structure. simple fix would be to use a normal instanced mesh (ISM) instead of an hism. that worked for me.
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