### 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)
Rect2i get_used_rect() const;
	
	void set_name(String p_name);
	String get_name() const;
	void set_enabled(bool p_enabled);
	bool is_enabled() const;
	void set_modulate(Color p_modulate);
	Color get_modulate() const;
	void set_y_sort_enabled(bool p_y_sort_enabled);
	bool is_y_sort_enabled() const;
	void set_y_sort_origin(int p_y_sort_origin);
	int get_y_sort_origin() const;
	void set_z_index(int p_z_index);
	int get_z_index() const;
	void set_navigation_enabled(bool p_enabled);
	bool is_navigation_enabled() const;
	void set_navigation_map(RID p_map);
	RID get_navigation_map() const;
	
	void fix_invalid_tiles();
	
	bool has_body_rid(RID p_physics_body) const;
	Vector2i get_coords_for_body_rid(RID p_physics_body) const; 
	~TileMapLayer();
};
class TileMap : public Node2D {
	GDCLASS(TileMap, Node2D);
public:
	enum VisibilityMode {
		VISIBILITY_MODE_DEFAULT,