### 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
item_edited(col, p_item, p_button);
						} else if (p_button == MouseButton::WHEEL_DOWN) {
							p_item->set_range(col, c.val - c.step);
							item_edited(col, p_item, p_button);
						}
						
						bring_up_editor = false;
					} else {
						editor_text = String::num(p_item->cells[col].val, Math::range_step_decimals(p_item->cells[col].step));
						if (select_mode == SELECT_MULTI && get_viewport()->get_processed_events_count() == focus_in_id) {
							bring_up_editor = false;
						}
					}
				}
				click_handled = true;
			} break;
			case TreeItem::CELL_MODE_ICON: {
				bring_up_editor = false;
			} break;
			case TreeItem::CELL_MODE_CUSTOM: {
				edited_item = p_item;
				edited_col = col;
				bool on_arrow = x > col_width - theme_cache.select_arrow->get_width();
				custom_popup_rect = Rect2i(get_global_position() + Point2i(col_ofs, _get_title_button_height() + y_ofs + item_h - theme_cache.offset.y), Size2(get_column_width(col), item_h));
				if (on_arrow || !p_item->cells[col].custom_button) {
					emit_signal(SNAME("custom_popup_edited"), ((bool)(x >= (col_width - item_h / 2))));
				}
				if (!p_item->cells[col].custom_button || !on_arrow) {
					item_edited(col, p_item, p_button);
				}