### Godot version

4.2 6da4ad1

### System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

### Issue description

![image](https://github.com/godotengine/godot/assets/2223172/d65ab202-93dd-4d83-bcef-c2b34bfa23f3)

In 4.2 dev3:
![image](https://github.com/godotengine/godot/assets/2223172/8621ec24-65d4-490d-bfc1-7e6e8aa3606a)


### Steps to reproduce

1. Create a scene with some children
2. Instantiate it in another scene
3. Enable editable children

### Minimal reproduction project

N/A
TreeItem *which = tree->get_edited();
	ERR_FAIL_COND(!which);
	NodePath np = which->get_metadata(0);
	Node *n = get_node(np);
	ERR_FAIL_COND(!n);
	String new_name = which->get_text(0);
	_rename_node(n, new_name);
}
Node *SceneTreeEditor::get_selected() {
	return selected;
}
void SceneTreeEditor::set_marked(const HashSet<Node *> &p_marked, bool p_selectable, bool p_children_selectable) {
	if (tree_dirty) {
		_update_tree();
	}
	marked = p_marked;
	marked_selectable = p_selectable;
	marked_children_selectable = p_children_selectable;
	_update_tree();
}
void SceneTreeEditor::set_marked(Node *p_marked, bool p_selectable, bool p_children_selectable) {
	HashSet<Node *> s;
	if (p_marked) {
		s.insert(p_marked);
	}
	set_marked(s, p_selectable, p_children_selectable);
}
void SceneTreeEditor::set_filter(const String &p_filter) {