### 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 (show_all_nodes) {
		p_parent->set_visible(keep_for_children || keep);
	} else {
		// Show only selectable nodes, or parents of selectable.
		p_parent->set_visible(keep_for_children || selectable);
	}
	if (selectable) {
		p_parent->clear_custom_color(0);
		p_parent->set_selectable(0, true);
	} else if (keep_for_children) {
		p_parent->set_custom_color(0, get_theme_color(SNAME("disabled_font_color"), SNAME("Editor")));
		p_parent->set_selectable(0, false);
		p_parent->deselect(0);
	}
	if (editor_selection) {
		Node *n = get_node(p_parent->get_metadata(0));
		if (selectable) {
			if (p_scroll_to_selected && n && editor_selection->is_selected(n)) {
				tree->scroll_to_item(p_parent);
			}
		} else {
			if (n && p_parent->is_selected(0)) {
				editor_selection->remove_node(n);
				p_parent->deselect(0);
			}
		}
	}
	return p_parent->is_visible();
}
bool SceneTreeEditor::_item_matches_all_terms(TreeItem *p_item, PackedStringArray p_terms) {