### 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
} break;
		case NOTIFICATION_INTERNAL_PHYSICS_PROCESS: {
			if (drag_touching) {
				if (drag_touching_deaccel) {
					float pos = v_scroll->get_value();
					pos += drag_speed * get_physics_process_delta_time();
					bool turnoff = false;
					if (pos < 0) {
						pos = 0;
						turnoff = true;
						set_physics_process_internal(false);
						drag_touching = false;
						drag_touching_deaccel = false;
					}
					if (pos > (v_scroll->get_max() - v_scroll->get_page())) {
						pos = v_scroll->get_max() - v_scroll->get_page();
						turnoff = true;
					}
					v_scroll->set_value(pos);
					float sgn = drag_speed < 0 ? -1 : 1;
					float val = Math::abs(drag_speed);
					val -= 1000 * get_physics_process_delta_time();
					if (val < 0) {
						turnoff = true;
					}
					drag_speed = sgn * val;
					if (turnoff) {
						set_physics_process_internal(false);
						drag_touching = false;
						drag_touching_deaccel = false;