How could the "extended" provisions of the Patriot Act and the provisions a new USA Freedom Act exist at the same time if they contradict each other? That makes zero legal sense, of course.
The sunset clause refers to the new Act,
which is linked, here and expires on December 31, 2017. That's not an "extension" of the current Act, it's a sunset clause on the new Act (amending the prior sunset clauses, not extending).
Pretty much all Acts of Congress of these types have sunset clauses. A two-year sunset clause is pretty short, actually.
Anyway, it's a moot point since the new Act failed in the Senate and now everybody has to vote on extending the Patriot Act in full which has passed the last several times.
Look, I wish they'd get rid of the entire fucking Patriot Act but we are living in a military police state and 9/11 took away any hope of freedom of privacy in this country.