best way of fixing the glitch

i found a glitch in a sql db index frag job that was suppose to tell everyone that the indexes needed to be re-indexedunfortunately if was only doing the master database and was copied to over 200 servers over a 1 year agoSo i looking for what method would be best drop recreate or rebuild online one server I was looking at had over 3 billion indexes rowsor maybe there is a better way