### 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)
bool has_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from);
	void remove_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from);
	Array get_source_level_tile_proxies() const;
	Array get_coords_level_tile_proxies() const;
	Array get_alternative_level_tile_proxies() const;
	Array map_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) const;
	void cleanup_invalid_tile_proxies();
	void clear_tile_proxies();
	
	int add_pattern(Ref<TileMapPattern> p_pattern, int p_index = -1);
	Ref<TileMapPattern> get_pattern(int p_index);
	void remove_pattern(int p_index);
	int get_patterns_count();
	
	RBSet<TerrainsPattern> get_terrains_pattern_set(int p_terrain_set);
	RBSet<TileMapCell> get_tiles_for_terrains_pattern(int p_terrain_set, TerrainsPattern p_terrain_tile_pattern);
	TileMapCell get_random_tile_from_terrains_pattern(int p_terrain_set, TerrainsPattern p_terrain_tile_pattern);
	
	Vector<Vector2> get_tile_shape_polygon();
	void draw_tile_shape(CanvasItem *p_canvas_item, Transform2D p_transform, Color p_color, bool p_filled = false, Ref<Texture2D> p_texture = Ref<Texture2D>());
	Vector<Point2> get_terrain_polygon(int p_terrain_set);
	Vector<Point2> get_terrain_peering_bit_polygon(int p_terrain_set, TileSet::CellNeighbor p_bit);
	void draw_terrains(CanvasItem *p_canvas_item, Transform2D p_transform, const TileData *p_tile_data);
	Vector<Vector<Ref<Texture2D>>> generate_terrains_icons(Size2i p_size);
	
	virtual void reset_state() override;
	TileSet();
	~TileSet();
};
class TileSetSource : public Resource {