Sections which are disabled on skeletal meshes still render when rendering skeletal meshes using nanite.
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I have the following hotfix in engine code (NaniteResources.cpp:2469) which appears to fix the issue, though I am not sure if that is the correct way to go about it:
// If Section is hidden, do not cast shadow
MaterialSection.bHidden = MeshObject->IsMaterialHidden(FirstLODIndex, MaterialSection.MaterialIndex);
// CHANGED CODE
MaterialSection.bHidden |= MeshSection.bDisabled;
// END CHANGED CODE
// If the material is NULL, or isn't flagged for use with skeletal meshes, it will be replaced by the default material.
UMaterialInterface* ShadingMaterial = InMeshDesc.GetMaterial(MaterialSection.MaterialIndex);