### 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)
PropertyInfo property_info;
	
	if (tile_set) {
		
		p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Rendering", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
		for (int i = 0; i < occluders.size(); i++) {
			
			property_info = PropertyInfo(Variant::OBJECT, vformat("occlusion_layer_%d/%s", i, PNAME("polygon")), PROPERTY_HINT_RESOURCE_TYPE, "OccluderPolygon2D", PROPERTY_USAGE_DEFAULT);
			if (!occluders[i].is_valid()) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			p_list->push_back(property_info);
		}
		
		p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Physics", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
		for (int i = 0; i < physics.size(); i++) {
			p_list->push_back(PropertyInfo(Variant::VECTOR2, vformat("physics_layer_%d/%s", i, PNAME("linear_velocity")), PROPERTY_HINT_NONE));
			p_list->push_back(PropertyInfo(Variant::FLOAT, vformat("physics_layer_%d/%s", i, PNAME("angular_velocity")), PROPERTY_HINT_NONE));
			p_list->push_back(PropertyInfo(Variant::INT, vformat("physics_layer_%d/%s", i, PNAME("polygons_count")), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_EDITOR));
			for (int j = 0; j < physics[i].polygons.size(); j++) {
				
				property_info = PropertyInfo(Variant::ARRAY, vformat("physics_layer_%d/polygon_%d/%s", i, j, PNAME("points")), PROPERTY_HINT_ARRAY_TYPE, "Vector2", PROPERTY_USAGE_DEFAULT);
				if (physics[i].polygons[j].polygon.is_empty()) {
					property_info.usage ^= PROPERTY_USAGE_STORAGE;
				}
				p_list->push_back(property_info);