### 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
switch (p_what) {
		case NOTIFICATION_FOCUS_ENTER: {
			if (get_viewport()) {
				focus_in_id = get_viewport()->get_processed_events_count();
			}
		} break;
		case NOTIFICATION_MOUSE_EXIT: {
			if (cache.hover_type != Cache::CLICK_NONE) {
				cache.hover_type = Cache::CLICK_NONE;
				queue_redraw();
			}
		} break;
		case NOTIFICATION_VISIBILITY_CHANGED: {
			drag_touching = false;
		} break;
		case NOTIFICATION_DRAG_END: {
			drop_mode_flags = 0;
			scrolling = false;
			set_physics_process_internal(false);
			queue_redraw();
		} break;
		case NOTIFICATION_DRAG_BEGIN: {
			single_select_defer = nullptr;
			if (theme_cache.scroll_speed > 0) {
				scrolling = true;
				set_physics_process_internal(true);
			}