The Season 4 premiere revealed that Sara had actually escaped from Gretchen's custody. The explanation for the previous season's evidence was that:
The decision to kill Sara was primarily driven by real-world factors rather than purely creative ones: prison break is sara really dead
After escaping her captors, she fled to Chicago and was kept safe by her father’s former aide, Bruce Bennett. Why Was She "Killed" in the First Place? The Season 4 premiere revealed that Sara had
Horrified by the sight, Lincoln never closely inspected the head to verify it was actually Sara. Horrified by the sight, Lincoln never closely inspected
In Season 3, Episode 4, titled "Good Fences," Lincoln Burrows finds a package containing what appears to be Sara’s severed head. This served as a brutal warning from The Company and its operative, Gretchen Morgan, to ensure Michael Scofield successfully broke James Whistler out of Sona prison. For the remainder of the season, characters and fans alike believed Sara had been murdered. The Season 4 Retcon