### 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 _test_update_tree();
	bool _update_filter(TreeItem *p_parent = nullptr, bool p_scroll_to_selected = false);
	bool _item_matches_all_terms(TreeItem *p_item, PackedStringArray p_terms);
	void _tree_changed();
	void _tree_process_mode_changed();
	void _node_removed(Node *p_node);
	void _node_renamed(Node *p_node);
	TreeItem *_find(TreeItem *p_node, const NodePath &p_path);
	void _notification(int p_what);
	void _selected_changed();
	void _deselect_items();
	void _rename_node(Node *p_node, const String &p_name);
	void _cell_collapsed(Object *p_obj);
	uint64_t last_hash;
	bool can_rename;
	bool can_open_instance;
	bool updating_tree = false;
	bool show_enabled_subscene = false;
	bool is_scene_tree_dock = false;
	void _renamed();
	HashSet<Node *> marked;
	bool marked_selectable = false;
	bool marked_children_selectable = false;
	bool display_foreign = false;
	bool tree_dirty = true;
	bool pending_test_update = false;
	static void _bind_methods();
	void _cell_button_pressed(Object *p_item, int p_column, int p_id, MouseButton p_button);
	void _toggle_visible(Node *p_node);
	void _cell_multi_selected(Object *p_object, int p_cell, bool p_selected);