### 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)

EditorPluginList *over_plugin_list = EditorNode::get_singleton()->get_editor_plugins_over();
	if (!over_plugin_list->is_empty()) {
		over_plugin_list->forward_3d_draw_over_viewport(surface);
	}
	EditorPluginList *force_over_plugin_list = EditorNode::get_singleton()->get_editor_plugins_force_over();
	if (!force_over_plugin_list->is_empty()) {
		force_over_plugin_list->forward_3d_force_draw_over_viewport(surface);
	}
	if (surface->has_focus()) {
		Size2 size = surface->get_size();
		Rect2 r = Rect2(Point2(), size);
		get_theme_stylebox(SNAME("FocusViewport"), EditorStringName(EditorStyles))->draw(surface->get_canvas_item(), r);
	}
	if (cursor.region_select) {
		const Rect2 selection_rect = Rect2(cursor.region_begin, cursor.region_end - cursor.region_begin);
		surface->draw_rect(
				selection_rect,
				get_theme_color(SNAME("box_selection_fill_color"), EditorStringName(Editor)));
		surface->draw_rect(
				selection_rect,
				get_theme_color(SNAME("box_selection_stroke_color"), EditorStringName(Editor)),
				false,
				Math::round(EDSCALE));
	}
	RID ci = surface->get_canvas_item();
	if (message_time > 0) {
		Ref<Font> font = get_theme_font(SNAME("font"), SNAME("Label"));