PHILADELPHIA Prosecuting Msgr. William J. Lynn was never going to be an open-and-shut case.

As far back as 2005, after scores of alleged victims told a grand jury about being abused by Philadelphia-area priests, prosecutors were divided over whether criminal charges would stick against the archdiocese's former secretary for clergy.

"Every prosecutor who looked at it could say, factually, these guys were endangering children," said Will Spade, an assistant district attorney at the time. "But some people thought the [state's child-endangerment] statute didn't apply, and others thought it did."

The debate resurfaced last week when Superior Court reversed Lynn's 2012 conviction on endangerment charges.

In a 43-page opinion released Thursday, the panel found that the Philadelphia prosecutors who ultimately charged Lynn two years ago and the trial judge who presided over his case had misapplied the law, which did not cover supervisors like Lynn until 2007.

That was three years after Lynn left the archdiocesean administration, and almost a decade after, prosecutors say, he let a priest with a history of abuse live at a Northeast Philadelphia parish, where he assaulted an altar boy.

The appellate court said there was more than enough evidence that Lynn had "prioritized the archdiocese's reputation over the safety of potential victims of sexually abusive priests," but not enough evidence to prove that he endangered children under the old law.

As the week ended, Lynn's fate was unclear.

On Monday, lawyers from the office of District Attorney Seth Williams are scheduled to ask Common Pleas Court Judge M. Teresa Sarmina, who sentenced Lynn to three to six years in prison, to keep him there while they appeal the ruling.

Tasha Jamerson, a spokeswoman for the DA's office, said prosecutors had no doubts about Lynn's guilt under the law when they charged him in 2012. Unlike the 2005 investigation, the DA's office had new evidence and a new victim who was abused by a priest under Lynn's supervision, Jamerson said. And that priest, Edward Avery, went on to plead guilty.

"We have no doubt that Lynn is guilty and his prosecution was proper," Jamerson said.

Lynn's lawyers, who challenged the law before and after the trial, will argue that he deserves bail.

Experts say the case may be the last chance for Philadelphia prosecutors to hold church administrators accountable for their role in decades-old abuses. But it's debatable whether it will have a larger impact moving forward.

Since Lynn's tenure, the Catholic Church has made significant changes to prevent abusive priests from staying in active ministry. And Pennsylvania strengthened its child-endangerment law in 2007 so that it applies to supervisors, such as Lynn, who oversee people in charge of children.

"I don't think, going forward, we're going to see many prosecutions of the same kind," said Nicholas Cafardi, a professor and canon-law expert at Duquesne University in Pittsburgh. "The law in the church is very clear. You can't put those guys back in the ministry. You have to be a heartless egotist to think you won't suffer the consequences."

Other church officials have been charged since Lynn. For instance, Bishop Robert W. Finn of Kansas City, Mo., was convicted last year and sentenced to probation for failing to report child abuse when hundreds of lewd photos were found on the laptop computer of one of his priests.

The Rev. Raymond C. O'Brien, a law professor at the Catholic University of America, said every priest and diocese is aware of those cases, and shuffling or concealing is no longer an option. "The days are gone when you're going to ship [abusive priests] off to be cured for six months and then let them come back as if nothing happened," O'Brien said.

O'Brien also said the Lynn case is not as significant as civil cases over the last decade in which church officials or dioceses were found liable for clergy sex abuse and ordered to pay millions of dollars.

"After 2004, there were huge economic repercussions, and that got the hierarchy's attention," he said.

Jeff Anderson, a Minnesota-based lawyer who represents several alleged victims suing the Philadelphia Archdiocese, said the Lynn case had a significant effect on the public's consciousness, conviction or not.

"The reversal of a conviction doesn't change a known truth," Anderson said. "It doesn't change the reality that is now known, that Lynn and top officials engaged in corrupt practices to protect their reputation over the peril of children."

During Lynn's trial, prosecutors exposed decades of child-abuse complaints involving Philadelphia-area priests - files that had been locked in a safe in church offices. The assistant district attorneys said it was necessary to establish that Lynn's decisions followed a practice or pattern among church leaders.

Taking the stand in his own defense, Lynn, a former top aide to Cardinal Anthony J. Bevilacqua, asserted that he lacked the authority to remove abusive priests, and did all he could and much more than his predecessors to keep them away from children.

"I thought I was helping people," Lynn testified. "I thought I was helping priests, and in those circumstances, I thought I was helping victims, as much as I could."

Jurors deliberated nearly 13 days before convicting him.

Spade, the former prosecutor, said the office had been divided in 2005 over whether a conviction was even possible.

"We looked at a lot of different legal theories, including a racketeering theory and obstruction of justice," said Spade, who is now a defense attorney. "We looked at everything to see if we could fit anything into existing law. The only thing that came close" was the endangering the welfare of a child statute.

But a grand jury and then-District Attorney Lynne M. Abraham passed on pressing charges that year.

"Unfortunately, the law currently stands in the way of justice for the victims of childhood sexual abuse," the grand jury report said.

Spade said the legal obstacles back then were frustrating. So, too, might be last week's decision, to others.

"I would think that all of those victims out there who were still looking for some sort of justice would be pretty disappointed right now," he said.

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Inquirer staff writer Allison Steele contributed to this article.