Lynn, who won an appeal of his landmark conviction, left state prison on Thursday after serving 18 months of a 3 to 6 year prison term. The Philadelphia District Attorney's Office is now trying to overturn the appeal.
Lynn left the prison in Waymart in northeastern Pennsylvania, prison spokeswoman Terri Fazio said, and was then taken by the Philadelphia Sheriff's Office to a city jail, where he was fitted with an electronic monitoring device.
Lynn, 62, was the first U.S. church official ever charged for hiding complaints that priests were molesting children. He was the point person for those complaints in Philadelphia from 1992-2004.
Prosecutors charged him with felony child endangerment. But the appeals court said the law that existed at the time didn't cover people who don't directly supervise children.
Lynn's lawyers, including Jeffrey Lindy and Alan Tauber, had made that argument even before his 2011 indictment, but Common Pleas Judge M. Teresa Sarmina sent the case to trial.
The Philadelphia archdiocese has been in the crosshairs of city prosecutors since 2002, when the priest-abuse scandal broke in Boston. Lynn, Cardinal Anthony Bevilacqua and other church officials - accompanied by lawyers - were grilled for days by an earlier grand jury that issued a damning report in 2005 but concluded that no charges could be filed.
Prosecutors tried again under District Attorney Seth Williams, who charged three priests with new sexual assault allegations in 2011 and Lynn with protecting the accused predators by hiding complaints in secret files. Bevilacqua, by then frail and elderly, was a potential witness in Lynn's case but died before trial. By that time, his mild-mannered successor, Cardinal Anthony Rigali, had been replaced in Philadelphia by dynamic Archbishop Charles Chaput.
Chaput has twice visited Lynn in prison and has said that no one person should become the scapegoat for the abuse crisis. Bergstrom, his attorney, said Lynn has become just that.
"There's clearly some reason to believe that that's what happened here," Bergstrom said.
Lynn, at his July 2012 sentencing, told Sarmina he tried his best to address the festering sex-abuse problem. He also voiced regret over his climb up the archdiocesan hierarchy.
"I am a parish priest. I should have stayed (one)," Lynn said.
Sarmina acknowledged that Lynn sometimes sent accused priests for therapy, but she said he ultimately protected the church's reputation over the souls of children. She sentenced him to three-to-six years in prison.
Lynn's conviction stems from the transfer of accused priest Edward Avery to a new parish, where he was later accused of raping a former altar boy in the church sacristy. Avery pleaded guilty and is serving 2 1/2- to five years in prison, although he denied the assault when called to testify at Lynn's trial.
Lynn remains a priest in good standing with the church, and could return to ministry. He last served as pastor of St. Joseph's in Downingtown, an affluent suburban parish whose members supported Lynn at his trial.
Information provided by the Associated Press was used in this article.