They left because Twitter started demanding thousands of dollars for organizations to maintain 'verified' status. Not just journalism outfits, but any 'organization,' to include e.g. popular web comics.
NPR decided the value prop wasn't worth the fee. This article seems to indicate they made the right call, from a dollars/engagement ratio.
It wasn't just that. Twitter labeled them as "state-affiliated media" and threatened to do all kinds of other nonsense like give their account away.