It used to be you'd lose all your achievements if going from one faction to the other, along with all the reps associated with vanguard rep. They fixed that this xpac (finally) so the only thing you have to redo is Sunreavers/Silver Covenant rep and that's not too difficult to regain. Also, going from Alliance to Horde there's a Tranquillien rep you need to get, but no ideas what the Alliance equivalent is tbh. You keep all the world event achievements (yay) for ARgent Tournament now though.