Lynn, 62, was released from a Northeastern Pennsylvania prison on Thursday and taken to Philadelphia to have his electronic monitoring arranged. He walked out of jail a free man on Friday, following 18 months in prison for a child-endangerment conviction that was overturned by an appeals court last week.
Lynn had been sentenced to three to six years in prison for his role in enabling priests to harm children.
Lynn's lawyer, Thomas A. Bergstrom, declined to say where Lynn would live while the Philadelphia District Attorney's Office pursues an appeal of last week's decision.
Victim rights groups and District Attorney Seth Williams have criticized the archdiocese for paying Lynn's bail.
"Chaput's action sends the worst possible message to current and former Catholic employees: No matter how recklessly, callously, and deceitfully you [endanger] kids and protect predators, the Catholic hierarchy will help you," Barbara Dorris of the St. Louis-based Survivors Network of Those Abused by Priests said this week.
Chaput's letter said the church remained committed to helping survivors of sexual abuse to heal.
"The Superior Court ruling does not vindicate Msgr. Lynn's past decisions," the letter stated. "Nor does it absolve the archdiocese from deeply flawed thinking and actions in the past that resulted in bitter suffering for victims of sexual abuse and their families."
Lynn is scheduled to appear Monday before Common Pleas Court Judge M. Teresa Sarmina, who in 2012 oversaw the case against him and sentenced him to prison. After setting his bail at $250,000 on Monday, the judge ordered Lynn to come to court so she could outline his bail conditions face-to-face.
Lynn is required to wear an electronic monitoring device and to report weekly to a parole officer, and he has surrendered his passport. Unless Lynn fails to appear for court or otherwise violates the terms of his release, most of the bail money will be returned when his case is resolved.
Lynn, who supervised priests as the archdiocesan secretary for clergy, was the first Catholic Church official in the country to be tried and imprisoned for crimes related to sex abuse in the church.
After a three-month trial, Lynn was convicted of endangering children in the late 1990s by allowing a sexually abusive priest to live and celebrate Mass at a Northeast Philadelphia parish, where the priest later assaulted an altar boy.
The Superior Court panel reversed the conviction, finding that prosecutors and the judge had misapplied the state's child-endangerment law when they prosecuted Lynn. Not until 2007 could supervisors such as Lynn be held criminally responsible under the endangerment law, the higher court found.
"I understand and accept the anger felt toward the archdiocese by many of our people and priests, as well as the general public, for the ugly events of the past decade," Chaput said in the letter. "Only time and a record of honest conversion by the archdiocese can change that.
"Msgr. Lynn has already spent 18 months in prison on a conviction which Pennsylvania's state appellate court has reversed - unanimously - as 'fundamentally flawed.' This reversal is not a matter of technicalities but of legal substance."
Ken Gavin, spokesman for the archdiocese, said Lynn has been on administrative leave since March 2011, and declined to comment as to whether Lynn could return to active ministry.