### 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)
void set_transpose(bool p_transpose);
	bool get_transpose() const;
	void set_texture_origin(Vector2i p_texture_origin);
	Vector2i get_texture_origin() const;
	void set_material(Ref<Material> p_material);
	Ref<Material> get_material() const;
	void set_modulate(Color p_modulate);
	Color get_modulate() const;
	void set_z_index(int p_z_index);
	int get_z_index() const;
	void set_y_sort_origin(int p_y_sort_origin);
	int get_y_sort_origin() const;
	void set_occluder(int p_layer_id, Ref<OccluderPolygon2D> p_occluder_polygon);
	Ref<OccluderPolygon2D> get_occluder(int p_layer_id) const;
	
	void set_constant_linear_velocity(int p_layer_id, const Vector2 &p_velocity);
	Vector2 get_constant_linear_velocity(int p_layer_id) const;
	void set_constant_angular_velocity(int p_layer_id, real_t p_velocity);
	real_t get_constant_angular_velocity(int p_layer_id) const;
	void set_collision_polygons_count(int p_layer_id, int p_shapes_count);
	int get_collision_polygons_count(int p_layer_id) const;
	void add_collision_polygon(int p_layer_id);
	void remove_collision_polygon(int p_layer_id, int p_polygon_index);
	void set_collision_polygon_points(int p_layer_id, int p_polygon_index, Vector<Vector2> p_polygon);
	Vector<Vector2> get_collision_polygon_points(int p_layer_id, int p_polygon_index) const;
	void set_collision_polygon_one_way(int p_layer_id, int p_polygon_index, bool p_one_way);
	bool is_collision_polygon_one_way(int p_layer_id, int p_polygon_index) const;
	void set_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index, float p_one_way_margin);
	float get_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index) const;
	int get_collision_polygon_shapes_count(int p_layer_id, int p_polygon_index) const;