Safest and recommended way to clean smartstor is to prune using smtartstor tool. by doing prune only metrics without data will be remove and your metrics with data will be safe. For pruning you have to stop EM and run prune command and start again.
If you don't care about the metrics with data and have lots of old ***.data files in your /data/archive folder you can delete some old dated files and restart your EMs.