### 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
if (EditorNode::get_singleton()->is_exiting()) {
		return; //speed up exit
	}
	if (p_node->is_connected("script_changed", callable_mp(this, &SceneTreeEditor::_node_script_changed))) {
		p_node->disconnect("script_changed", callable_mp(this, &SceneTreeEditor::_node_script_changed));
	}
	if (p_node->is_class("Node3D") || p_node->is_class("CanvasItem") || p_node->is_class("CanvasLayer") || p_node->is_class("Window")) {
		if (p_node->is_connected("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed))) {
			p_node->disconnect("visibility_changed", callable_mp(this, &SceneTreeEditor::_node_visibility_changed));
		}
	}
	if (p_node == selected) {
		selected = nullptr;
		emit_signal(SNAME("node_selected"));
	}
}
void SceneTreeEditor::_node_renamed(Node *p_node) {
	if (p_node != get_scene_node() && !get_scene_node()->is_ancestor_of(p_node)) {
		return;
	}
	emit_signal(SNAME("node_renamed"));
	if (!tree_dirty) {
		MessageQueue::get_singleton()->push_call(this, "_update_tree");
		tree_dirty = true;
	}
}
void SceneTreeEditor::_update_tree(bool p_scroll_to_selected) {