### 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)

xform_hbc = memnew(HBoxContainer);
	xform_vbc->add_child(xform_hbc);
	for (int i = 0; i < 3; i++) {
		xform_scale[i] = memnew(LineEdit);
		xform_scale[i]->set_h_size_flags(SIZE_EXPAND_FILL);
		xform_scale[i]->set_select_all_on_focus(true);
		xform_hbc->add_child(xform_scale[i]);
	}
	l = memnew(Label);
	l->set_text(TTR("Transform Type"));
	xform_vbc->add_child(l);
	xform_type = memnew(OptionButton);
	xform_type->set_h_size_flags(SIZE_EXPAND_FILL);
	xform_type->add_item(TTR("Pre"));
	xform_type->add_item(TTR("Post"));
	xform_vbc->add_child(xform_type);
	xform_dialog->connect("confirmed", callable_mp(this, &Node3DEditor::_xform_dialog_action));
	selected = nullptr;
	set_process_shortcut_input(true);
	add_to_group("_spatial_editor_group");
	EDITOR_DEF("editors/3d/manipulator_gizmo_size", 80);
	EditorSettings::get_singleton()->add_property_hint(PropertyInfo(Variant::INT, "editors/3d/manipulator_gizmo_size", PROPERTY_HINT_RANGE, "16,160,1"));
	EDITOR_DEF("editors/3d/manipulator_gizmo_opacity", 0.9);
	EditorSettings::get_singleton()->add_property_hint(PropertyInfo(Variant::FLOAT, "editors/3d/manipulator_gizmo_opacity", PROPERTY_HINT_RANGE, "0,1,0.01"));
	EDITOR_DEF("editors/3d/navigation/show_viewport_rotation_gizmo", true);
	EDITOR_DEF("editors/3d/navigation/show_viewport_navigation_gizmo", DisplayServer::get_singleton()->is_touchscreen_available());
	current_hover_gizmo_handle = -1;
	current_hover_gizmo_handle_secondary = false;
	{
		/