This is the response from someone associated with the production:
Daniel was NOT exonerated - that is, tried and found not guilty. He was tried, convicted and then his conviction was "vacated" or set aside -- it's not a "not guilty" verdict, it 's like an after-the-fact mistrial, as if no trial had happened at all, which leaves Daniel as vulnerable to retrial as if he'd never been tried at all.
Daniel was tried and convicted based on a single assailant theory (meaning he was purportedly the sole perpetrator of the rape and murder) so that once they find multiple sperm samples on Hanna's underwear (this is something Jon Stern pushes through years into Daniel's incarceration) the prosecuting theory is then disqualified, and he is then released until the state decides if they are going to retry him with a different theory that addresses the multiple sperm samples.
I ran that explanation past friend-of-Tuned-In-Journal Legal Eagle to get his take:
It’s out of my area of expertise, but it still sounds super fishy.
It’s true that a state can re-try a defendant when his conviction was vacated on a procedural error at trial. So, when the prosecution fails to turn over certain evidence, the court can vacate the resulting conviction, and the defendant can be retried with the proper evidence turn-over.
But the facts of this story seem different. If they have a sample of his DNA, and it doesn’t match the DNA on the girl, and he’s released, then he is released under an actual innocence exoneration from the Due Process Clause. (This would not be a mere vacation on a technicality.) Just as due process would require his release from prison, due process/double jeopardy would also prohibit him being re-charged with the same crime.
On the other hand, if his sample DNA does match the DNA on the girl, and there just happens to be somebody else’s DNA on the girl too, then he doesn’t get released. Rather, that just confirms his guilt and indicates that somebody else was in on the job.
This is still a gaping plot hole.