The Wikipedia article is quite confusing, and seems to imply that those two provisions expired because they were the only two provisions not sunsetted already. The table indicates that most of the law sunsetted on March of 2006:

https://en.wikipedia.org/wiki/Patriot_Act#Section_expiration...

But then they say "The first act reauthorized all but two Title II provisions. Two sections were changed to sunset on December 31, 2009"

But the first act was passed in 2005, and so it's unclear whether it reauthorized provisions only until 2006 or a longer term.