Lynn's lawyer, Thomas A. Bergstrom, said the move by Williams' office was not entirely unexpected.
"This is like a never-ending saga," he said. "Hopefully, the Superior Court's opinion will stand."
In tossing Lynn's conviction last week, Superior Court took issue with evidence prosecutors introduced at Lynn's 2012 trial in an attempt to prove that the Philadelphia Archdiocese historically mishandled child-abuse complaints involving area priests.
Some files shown to jurors from the archdiocese's "secret archive" dated back to the 1940s, preceding by decades Lynn's tenure as the official in charge of handling sex abuse cases.
Lynn had been charged with mishandling decisions involving one specific priest - the Rev. Edward J. Avery - who had a history of sexually abusing children. Despite previous allegations against Avery, Lynn allowed him to live in a Northeast rectory, where he later assaulted a 10-year-old altar boy. Avery pleaded guilty to the 1999 attack and is serving five years in prison.
Common Pleas Court Judge M. Teresa Sarmina, who presided over Lynn's original trial, ruled that the historic evidence of the church's treatment of accused priests offered insight into Lynn's decision-making once he took over as the archdiocese's secretary for clergy in 1992. It also shed light on the archdiocese's practice of protecting its own institutional interests by covering up abuse complaints, Sarmina found.
However, Judge Emeritus John T. Bender, writing for the Superior Court majority last week, described such evidence as "unfairly prejudicial," and sided with Lynn's argument that it effectively turned him into a scapegoat for the wider sins of the church.
Williams defended Sarmina's decision at a news conference Monday in which he sought to couch the case in a larger discussion of child sex abuse involving perpetrators who are known to their victims.
"The evidence presented at trial showed the jury and the world that [Lynn's] handling of Father Avery was completely typical of his handling of other similar predator priests and established that he knew just how dangerous such priests were," he said.
If pressed, the district attorney added, his office was prepared to try the case against Lynn again in Common Pleas Court.
Lynn remains housed in a state prison in Waymart, northeast of Scranton, having completed more than two years of his three- to six-year term.
The same appellate court panel tossed Lynn's conviction once before, finding in 2013 that he had been improperly charged under a law that did not apply at the time of his alleged crimes. That legal victory was short-lived, as the Pennsylvania Supreme Court overturned that decision and reinstated the jury's guilty verdict this year.
Last week's Superior Court ruling threw out Lynn's conviction under a different argument - one of 10 made by his lawyers - but did not address Lynn's eight remaining claims.
In its court filings Monday, Williams' office urged Superior Court to settle all 10 of the monsignor's arguments to prevent "years of unnecessary litigation" as the case moves between the appellate courts.
In the meantime, Bergstrom, Lynn's lawyer, has petitioned Sarmina to order his client's release.
A hearing on that request has not yet been scheduled, but Williams said Monday he planned to push back against it.