### 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)

add_gizmo_plugin(Ref<VisibleOnScreenNotifier3DGizmoPlugin>(memnew(VisibleOnScreenNotifier3DGizmoPlugin)));
	add_gizmo_plugin(Ref<GPUParticles3DGizmoPlugin>(memnew(GPUParticles3DGizmoPlugin)));
	add_gizmo_plugin(Ref<GPUParticlesCollision3DGizmoPlugin>(memnew(GPUParticlesCollision3DGizmoPlugin)));
	add_gizmo_plugin(Ref<CPUParticles3DGizmoPlugin>(memnew(CPUParticles3DGizmoPlugin)));
	add_gizmo_plugin(Ref<ReflectionProbeGizmoPlugin>(memnew(ReflectionProbeGizmoPlugin)));
	add_gizmo_plugin(Ref<DecalGizmoPlugin>(memnew(DecalGizmoPlugin)));
	add_gizmo_plugin(Ref<VoxelGIGizmoPlugin>(memnew(VoxelGIGizmoPlugin)));
	add_gizmo_plugin(Ref<LightmapGIGizmoPlugin>(memnew(LightmapGIGizmoPlugin)));
	add_gizmo_plugin(Ref<LightmapProbeGizmoPlugin>(memnew(LightmapProbeGizmoPlugin)));
	add_gizmo_plugin(Ref<CollisionObject3DGizmoPlugin>(memnew(CollisionObject3DGizmoPlugin)));
	add_gizmo_plugin(Ref<CollisionShape3DGizmoPlugin>(memnew(CollisionShape3DGizmoPlugin)));
	add_gizmo_plugin(Ref<CollisionPolygon3DGizmoPlugin>(memnew(CollisionPolygon3DGizmoPlugin)));
	add_gizmo_plugin(Ref<NavigationLink3DGizmoPlugin>(memnew(NavigationLink3DGizmoPlugin)));
	add_gizmo_plugin(Ref<NavigationRegion3DGizmoPlugin>(memnew(NavigationRegion3DGizmoPlugin)));
	add_gizmo_plugin(Ref<Joint3DGizmoPlugin>(memnew(Joint3DGizmoPlugin)));
	add_gizmo_plugin(Ref<PhysicalBone3DGizmoPlugin>(memnew(PhysicalBone3DGizmoPlugin)));
	add_gizmo_plugin(Ref<FogVolumeGizmoPlugin>(memnew(FogVolumeGizmoPlugin)));
}
void Node3DEditor::_bind_methods() {
	ClassDB::bind_method("_get_editor_data", &Node3DEditor::_get_editor_data);
	ClassDB::bind_method("_request_gizmo", &Node3DEditor::_request_gizmo);
	ClassDB::bind_method("_request_gizmo_for_id", &Node3DEditor::_request_gizmo_for_id);
	ClassDB::bind_method("_set_subgizmo_selection", &Node3DEditor::_set_subgizmo_selection);
	ClassDB::bind_method("_clear_subgizmo_selection", &Node3DEditor::_clear_subgizmo_selection);
	ClassDB::bind_method("_refresh_menu_icons", &Node3DEditor::_refresh_menu_icons);
	ADD_SIGNAL(MethodInfo("transform_key_request"));
	ADD_SIGNAL(MethodInfo("item_lock_status_changed"));
	ADD_SIGNAL(MethodInfo("item_group_status_changed"));
}
void Node3DEditor::clear() {