From the Ausiello report at TVGuide.com:
Prison Break fans, prepare to seriously lose your heads.
Sarah Wayne Callies — whose rather ugly contract dispute with producers led to her apparent decapitation last October — is returning next season. Full-time. As Dr. Sara Tancredi. Head and all. Seriously.
How? Why? When? WTF?! All legitimate questions. Good thing I just hung up with Mr. Answer Man (aka executive producer Matt Olmstead).
So… I take it that wasn’t Sara’s head in that box…
Matt Olmstead: Yeah, that wasn’t.
But initially it was supposed to be her head. What changed?
Olmstead: What changed was…. Click here for the full interview