Joe Dolson on "[Plugin: WP to Twitter] Create new URL"

The URL is saved in a custom post meta. If you go into the database and delete that custom post meta, it'll use the short URL instead.

Since you're asking about short URLs, I'd be interested in getting you input on the future of URL shortening in WP to Twitter:

http://www.joedolson.com/articles/2012/12/wp-to-twitter-the-next-step-forward/