### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
String name = tile_set->get_terrain_name(terrain_set, i);
			if (name.is_empty()) {
				options.push_back(vformat("Terrain %d", i));
			} else {
				options.push_back(name);
			}
		}
		terrain_property_editor->setup(options);
		terrain_property_editor->update_property();
		
		
		OptionButton *option_button = Object::cast_to<OptionButton>(terrain_property_editor->get_child(0));
		for (int terrain = 0; terrain < tile_set->get_terrains_count(terrain_set); terrain++) {
			option_button->set_item_icon(terrain + 1, icons[terrain_set][terrain]);
		}
		terrain_property_editor->show();
	}
}
void TileDataTerrainsEditor::_property_value_changed(StringName p_property, Variant p_value, StringName p_field) {
	Variant old_value = dummy_object->get(p_property);
	dummy_object->set(p_property, p_value);
	if (p_property == "terrain_set") {
		if (p_value != old_value) {
			dummy_object->set("terrain", -1);
		}
		_update_terrain_selector();
	}
	emit_signal(SNAME("needs_redraw"));
}
void TileDataTerrainsEditor::_tile_set_changed() {