### 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)
Ref<ConvexPolygonShape2D> get_collision_polygon_shape(int p_layer_id, int p_polygon_index, int shape_index) const;
	
	void set_terrain_set(int p_terrain_id);
	int get_terrain_set() const;
	void set_terrain(int p_terrain_id);
	int get_terrain() const;
	void set_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit, int p_terrain_id);
	int get_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const;
	bool is_valid_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const;
	TileSet::TerrainsPattern get_terrains_pattern() const; 
	
	void set_navigation_polygon(int p_layer_id, Ref<NavigationPolygon> p_navigation_polygon);
	Ref<NavigationPolygon> get_navigation_polygon(int p_layer_id) const;
	
	void set_probability(float p_probability);
	float get_probability() const;
	
	void set_custom_data(String p_layer_name, Variant p_value);
	Variant get_custom_data(String p_layer_name) const;
	void set_custom_data_by_layer_id(int p_layer_id, Variant p_value);
	Variant get_custom_data_by_layer_id(int p_layer_id) const;
};
VARIANT_ENUM_CAST(TileSet::CellNeighbor);
VARIANT_ENUM_CAST(TileSet::TerrainMode);
VARIANT_ENUM_CAST(TileSet::TileShape);
VARIANT_ENUM_CAST(TileSet::TileLayout);
VARIANT_ENUM_CAST(TileSet::TileOffsetAxis);
VARIANT_ENUM_CAST(TileSetAtlasSource::TileAnimationMode);
#endif