### 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
hash = hash_djb2_one_64(p_node->get_instance_id(), hash);
	if (p_node->get_parent()) {
		hash = hash_djb2_one_64(p_node->get_parent()->get_instance_id(), hash); //so a reparent still produces a different hash
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		_compute_hash(p_node->get_child(i), hash);
	}
}
void SceneTreeEditor::_test_update_tree() {
	pending_test_update = false;
	if (!is_inside_tree()) {
		return;
	}
	if (tree_dirty) {
		return; // don't even bother
	}
	uint64_t hash = hash_djb2_one_64(0);
	if (get_scene_node()) {
		_compute_hash(get_scene_node(), hash);
	}
	//test hash
	if (hash == last_hash) {
		return; // did not change
	}
	MessageQueue::get_singleton()->push_call(this, "_update_tree");
	tree_dirty = true;
}
void SceneTreeEditor::_tree_process_mode_changed() {