### Godot version

4.2 dev1

### 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

Calling `Tree.propagate_check()` after an item is unchecked does not properly uncheck the parents. They are left in partially checked state.

It's easy to observe in theme editor:

https://github.com/godotengine/godot/assets/2223172/71d0479c-0a5e-48d3-957f-d90379a95c22



### Steps to reproduce

1. Edit a Theme resource
2. Go to Manage Items... menu
3. Go to Import Items tab
4. Unfold something
5. Check and uncheck a child checkbox

### Minimal reproduction project

N/A
Rect2 rect = popup_edited_item->get_meta("__focus_rect");
				popup_editor->set_position(get_global_position() + rect.position);
				popup_editor->set_size(rect.size);
				popup_editor->child_controls_changed();
			}
		} break;
	}
}
void Tree::_update_all() {
	for (int i = 0; i < columns.size(); i++) {
		update_column(i);
	}
	if (root) {
		update_item_cache(root);
	}
}
Size2 Tree::get_minimum_size() const {
	if (h_scroll_enabled && v_scroll_enabled) {
		return Size2();
	} else {
		Vector2 min_size = get_internal_min_size();
		Ref<StyleBox> bg = theme_cache.panel_style;
		if (bg.is_valid()) {
			min_size.x += bg->get_margin(SIDE_LEFT) + bg->get_margin(SIDE_RIGHT);
			min_size.y += bg->get_margin(SIDE_TOP) + bg->get_margin(SIDE_BOTTOM);
		}
		return Vector2(h_scroll_enabled ? 0 : min_size.x, v_scroll_enabled ? 0 : min_size.y);
	}
}
TreeItem *Tree::create_item(TreeItem *p_parent, int p_index) {