Open the attached project in Design Studio and move cubes around in the navigator to change their parent-child relationships. Mix in multiselections on objects with different parents and make sure to not always move objects between same level parents. After some moves, materials start randomly getting corrupted. This manifests either with wrong material being used for the cube or cube becoming transparent. Transparent cubes are still there as they can be selected.

Reloading 3d edit view fixes the scene.