### 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
text_pos.x += cache.rtl ? sb->get_offset().x : tbrect.size.width - (sb->get_offset().x + columns[i].text_buf->get_size().x);
							break;
						}
						default: {
							text_pos.x += sb->get_offset().x + (tbrect.size.width - columns[i].text_buf->get_size().x) / 2;
							break;
						}
					}
					if (theme_cache.font_outline_size > 0 && theme_cache.font_outline_color.a > 0) {
						columns[i].text_buf->draw_outline(ci, text_pos, theme_cache.font_outline_size, theme_cache.font_outline_color);
					}
					columns[i].text_buf->draw(ci, text_pos, theme_cache.title_button_color);
				}
			}
			
			
			if (has_focus()) {
				RenderingServer::get_singleton()->canvas_item_add_clip_ignore(ci, true);
				theme_cache.focus_style->draw(ci, Rect2(Point2(), get_size()));
				RenderingServer::get_singleton()->canvas_item_add_clip_ignore(ci, false);
			}
		} break;
		case NOTIFICATION_THEME_CHANGED:
		case NOTIFICATION_LAYOUT_DIRECTION_CHANGED:
		case NOTIFICATION_TRANSLATION_CHANGED: {
			_update_all();
		} break;
		case NOTIFICATION_RESIZED:
		case NOTIFICATION_TRANSFORM_CHANGED: {
			if (popup_edited_item != nullptr) {