Complex sentence: The "Capitol Corridor" route was also known as the "Capitols", but in order to avoid confusion with the Amtrak "Capitol Limited" route from Washington, D.C. to Chicago, "Capitol Corridor" is now the official, preferred name.
Split into simpler sentences: The "Capitol Corridor" route is also known as the "Capitols". But in order to avoid confusion with the Amtrak "Capitol Limited" route from Washington, D.C. to Chicago, "Capitol Corridor" is now the official name and preferred name.