### 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)
ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	physics.write[p_layer_id].polygons.remove_at(p_polygon_index);
	emit_signal(SNAME("changed"));
}
void TileData::set_collision_polygon_points(int p_layer_id, int p_polygon_index, Vector<Vector2> p_polygon) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	ERR_FAIL_COND_MSG(p_polygon.size() != 0 && p_polygon.size() < 3, "Invalid polygon. Needs either 0 or more than 3 points.");
	if (p_polygon.is_empty()) {
		physics.write[p_layer_id].polygons.write[p_polygon_index].shapes.clear();
	} else {
		
		Vector<Vector<Vector2>> decomp = Geometry2D::decompose_polygon_in_convex(p_polygon);
		ERR_FAIL_COND_MSG(decomp.is_empty(), "Could not decompose the polygon into convex shapes.");
		physics.write[p_layer_id].polygons.write[p_polygon_index].shapes.resize(decomp.size());
		for (int i = 0; i < decomp.size(); i++) {
			Ref<ConvexPolygonShape2D> shape;
			shape.instantiate();
			shape->set_points(decomp[i]);
			physics.write[p_layer_id].polygons.write[p_polygon_index].shapes[i] = shape;
		}
	}
	physics.write[p_layer_id].polygons.write[p_polygon_index].polygon = p_polygon;
	emit_signal(SNAME("changed"));
}
Vector<Vector2> TileData::get_collision_polygon_points(int p_layer_id, int p_polygon_index) const {