### 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)
ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), RBSet<TileMapCell>());
	_update_terrains_cache();
	return per_terrain_pattern_tiles[p_terrain_set][p_terrain_tile_pattern];
}
TileMapCell TileSet::get_random_tile_from_terrains_pattern(int p_terrain_set, TileSet::TerrainsPattern p_terrain_tile_pattern) {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), TileMapCell());
	_update_terrains_cache();
	
	double sum = 0.0;
	RBSet<TileMapCell> set = per_terrain_pattern_tiles[p_terrain_set][p_terrain_tile_pattern];
	for (const TileMapCell &E : set) {
		if (E.source_id >= 0) {
			Ref<TileSetSource> source = sources[E.source_id];
			Ref<TileSetAtlasSource> atlas_source = source;
			if (atlas_source.is_valid()) {
				TileData *tile_data = atlas_source->get_tile_data(E.get_atlas_coords(), E.alternative_tile);
				sum += tile_data->get_probability();
			} else {
				sum += 1.0;
			}
		} else {
			sum += 1.0;
		}
	}
	
	double count = 0.0;