### 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)

rotation_control->set_viewport(this);
	top_right_vbox->add_child(rotation_control);
	/
	cpu_time_label = memnew(Label);
	top_right_vbox->add_child(cpu_time_label);
	cpu_time_label->hide();
	gpu_time_label = memnew(Label);
	top_right_vbox->add_child(gpu_time_label);
	gpu_time_label->hide();
	fps_label = memnew(Label);
	top_right_vbox->add_child(fps_label);
	fps_label->hide();
	surface->add_child(top_right_vbox);
	accept = nullptr;
	freelook_active = false;
	freelook_speed = EDITOR_GET("editors/3d/freelook/freelook_base_speed");
	selection_menu = memnew(PopupMenu);
	add_child(selection_menu);
	selection_menu->set_min_size(Size2(100, 0) * EDSCALE);
	selection_menu->connect("id_pressed", callable_mp(this, &Node3DEditorViewport::_selection_result_pressed));
	selection_menu->connect("popup_hide", callable_mp(this, &Node3DEditorViewport::_selection_menu_hide));
	if (p_index == 0) {
		view_menu->get_popup()->set_item_checked(view_menu->get_popup()->get_item_index(VIEW_AUDIO_LISTENER), true);
		viewport->set_as_audio_listener_3d(true);
	}
	view_type = VIEW_TYPE_USER;
	_update_name();
	EditorSettings::get_singleton()->connect("settings_changed", callable_mp(this, &Node3DEditorViewport::update_transform_gizmo_view));
}
Node3DEditorViewport::~Node3DEditorViewport() {