### Godot version

4.1-beta3

### System information

Windows

### Issue description

When an inherited scene's source has children, or when an instantiated scene is expanded with the editable children option in the scene tree dock, they are usually colored yellow. In beta3 this yellow color disappears under certain conditions. I've found it to happen when another scene is switched to through the tab menu, and then the current scene is opened again. It also happens when first opening the project. The text is colored yellow again when the scene is opened from file, or when it is edited from the scene tree dock.

### Steps to reproduce


https://github.com/godotengine/godot/assets/76705401/ae4a6314-873c-490d-9cc0-d85766702772



### Minimal reproduction project

Trivial
void _update_selection(TreeItem *item);
	void _node_script_changed(Node *p_node);
	void _node_visibility_changed(Node *p_node);
	void _update_visibility_color(Node *p_node, TreeItem *p_item);
	void _selection_changed();
	Node *get_scene_node();
	Variant get_drag_data_fw(const Point2 &p_point, Control *p_from);
	bool can_drop_data_fw(const Point2 &p_point, const Variant &p_data, Control *p_from) const;
	void drop_data_fw(const Point2 &p_point, const Variant &p_data, Control *p_from);
	void _empty_clicked(const Vector2 &p_pos, MouseButton p_button);
	void _rmb_select(const Vector2 &p_pos, MouseButton p_button = MouseButton::RIGHT);
	void _warning_changed(Node *p_for_node);
	Timer *update_timer = nullptr;
	List<StringName> *script_types;
	bool _is_script_type(const StringName &p_type) const;
	Vector<StringName> valid_types;
public:
	
	void _update_tree(bool p_scroll_to_selected = false);
	void set_filter(const String &p_filter);
	String get_filter() const;
	String get_filter_term_warning();
	void set_show_all_nodes(bool p_show_all_nodes);
	void set_as_scene_tree_dock();
	void set_display_foreign_nodes(bool p_display);
	void set_marked(const HashSet<Node *> &p_marked, bool p_selectable = false, bool p_children_selectable = true);
	void set_marked(Node *p_marked, bool p_selectable = false, bool p_children_selectable = true);
	void set_selected(Node *p_node, bool p_emit_selected = true);
	Node *get_selected();
	void set_can_rename(bool p_can_rename) { can_rename = p_can_rename; }