### 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_tile_set(const TileSet *p_tile_set);
	void notify_tile_data_properties_should_change();
	void add_occlusion_layer(int p_index);
	void move_occlusion_layer(int p_from_index, int p_to_pos);
	void remove_occlusion_layer(int p_index);
	void add_physics_layer(int p_index);
	void move_physics_layer(int p_from_index, int p_to_pos);
	void remove_physics_layer(int p_index);
	void add_terrain_set(int p_index);
	void move_terrain_set(int p_from_index, int p_to_pos);
	void remove_terrain_set(int p_index);
	void add_terrain(int p_terrain_set, int p_index);
	void move_terrain(int p_terrain_set, int p_from_index, int p_to_pos);
	void remove_terrain(int p_terrain_set, int p_index);
	void add_navigation_layer(int p_index);
	void move_navigation_layer(int p_from_index, int p_to_pos);
	void remove_navigation_layer(int p_index);
	void add_custom_data_layer(int p_index);
	void move_custom_data_layer(int p_from_index, int p_to_pos);
	void remove_custom_data_layer(int p_index);
	void set_allow_transform(bool p_allow_transform);
	bool is_allowing_transform() const;
	
	TileData *duplicate();
	
	void set_flip_h(bool p_flip_h);
	bool get_flip_h() const;
	void set_flip_v(bool p_flip_v);
	bool get_flip_v() const;