### 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)
};
	Vector<PhysicsLayer> physics_layers;
	
	struct Terrain {
		String name;
		Color color;
	};
	struct TerrainSet {
		TerrainMode mode = TERRAIN_MODE_MATCH_CORNERS_AND_SIDES;
		Vector<Terrain> terrains;
	};
	Vector<TerrainSet> terrain_sets;
	HashMap<TerrainMode, Ref<ArrayMesh>> terrain_meshes;
	HashMap<TerrainMode, HashMap<CellNeighbor, Ref<ArrayMesh>>> terrain_peering_bits_meshes;
	bool terrain_bits_meshes_dirty = true;
	LocalVector<RBMap<TileSet::TerrainsPattern, RBSet<TileMapCell>>> per_terrain_pattern_tiles; 
	bool terrains_cache_dirty = true;
	void _update_terrains_cache();
	
	struct NavigationLayer {
		uint32_t layers = 1;
	};
	Vector<NavigationLayer> navigation_layers;
	
	struct CustomDataLayer {
		String name;
		Variant::Type type = Variant::NIL;
	};
	Vector<CustomDataLayer> custom_data_layers;
	HashMap<String, int> custom_data_layers_by_name;