### Godot version

Master (4.2)

### System information

Windows 11 - Vulkan - Nvidia RTX 4070 - intel i5 13600KF

### Issue description

As you can see in the video when you try to add multiple scenes in to the 3D viewport (only with multiple scenes) the editor throws this error.

```
ERROR: Can't add child '@Node3D@18837' to '@SubViewport@9274', already has a parent '@SubViewport@9274'.
   at: (scene\main\node.cpp:1411)
```


Video: https://youtu.be/BVcCIigQJDw

This happens in the latest master (pulled on 2.11.2023).

### Steps to reproduce

Drag couple of the 3d mesh scenes into the 3D viewport and then select multiple scenes and drag them over and observer the error.

### Minimal reproduction project

[TestSceneDragAndDrop.zip](https://github.com/godotengine/godot/files/13253741/TestSceneDragAndDrop.zip)

plane_mat->set_flag(StandardMaterial3D::FLAG_DISABLE_FOG, true);
				plane_mat->set_on_top_of_alpha();
				plane_mat->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
				plane_mat->set_cull_mode(StandardMaterial3D::CULL_DISABLED);
				plane_mat->set_albedo(col);
				plane_gizmo_color[i] = plane_mat; /
				surftool->set_material(plane_mat);
				surftool->commit(scale_plane_gizmo[i]);
				Ref<StandardMaterial3D> plane_mat_hl = plane_mat->duplicate();
				plane_mat_hl->set_albedo(col.from_hsv(col.get_h(), 0.25, 1.0, 1));
				plane_gizmo_color_hl[i] = plane_mat_hl; /
			}
			/
			{
				Ref<SurfaceTool> surftool = memnew(SurfaceTool);
				surftool->begin(Mesh::PRIMITIVE_LINE_STRIP);
				Vector3 vec;
				vec[i] = 1;
				/
				surftool->add_vertex(vec * -1048576);
				surftool->add_vertex(Vector3());
				surftool->add_vertex(vec * 1048576);
				surftool->set_material(mat_hl);
				surftool->commit(axis_gizmo[i]);
			}
		}
	}
	_generate_selection_boxes();
}
void Node3DEditor::_update_gizmos_menu() {