### 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 set_editor_selection(EditorSelection *p_selection);
	void set_show_enabled_subscene(bool p_show) { show_enabled_subscene = p_show; }
	void set_valid_types(const Vector<StringName> &p_valid);
	void update_tree() { _update_tree(); }
	void set_auto_expand_selected(bool p_auto, bool p_update_settings);
	void set_connect_to_script_mode(bool p_enable);
	void set_connecting_signal(bool p_enable);
	Tree *get_scene_tree() { return tree; }
	void update_warning();
	SceneTreeEditor(bool p_label = true, bool p_can_rename = false, bool p_can_open_instance = false);
	~SceneTreeEditor();
};
class SceneTreeDialog : public ConfirmationDialog {