### 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)
struct PhysicsLayerTileData {
		struct PolygonShapeTileData {
			LocalVector<Vector2> polygon;
			LocalVector<Ref<ConvexPolygonShape2D>> shapes;
			bool one_way = false;
			float one_way_margin = 1.0;
		};
		Vector2 linear_velocity;
		double angular_velocity = 0.0;
		Vector<PolygonShapeTileData> polygons;
	};
	Vector<PhysicsLayerTileData> physics;
	
	
	int terrain_set = -1;
	int terrain = -1;
	int terrain_peering_bits[16] = { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 };
	
	Vector<Ref<NavigationPolygon>> navigation;
	
	double probability = 1.0;
	
	Vector<Variant> custom_data;
protected:
	bool _set(const StringName &p_name, const Variant &p_value);
	bool _get(const StringName &p_name, Variant &r_ret) const;
	void _get_property_list(List<PropertyInfo> *p_list) const;
	static void _bind_methods();
public: