Lynn, 61, became the nation's first Catholic church supervisor convicted for covering up abuse by a priest. Common Pleas Court Judge M. Teresa Sarmina revoked his bail and jailed him.
But the jury's protracted struggle and split decision reflect the legal tightrope the case had become.
The panel acquitted Lynn of conspiracy and a second endangerment count and failed to reach verdicts on attempted rape and endangerment charges against Lynn's co-defendant, the Rev. James J. Brennan.
It also rejected allegations that Lynn, who for 12 years as clergy secretary investigated abuse complaints and recommended priests' assignments, was part of a larger conspiracy to harm children.
Philadelphia District Attorney Seth Williams on Friday dismissed any suggestion the outcome was anything less than a validation of two grand jury investigations.
"I can assure you that as Msgr. Lynn sits in a holding cell right now, he got the message," Williams said. "And others will get the message as well."
Logan, a 35-year-old bank employee from West Philadelphia, said jurors who switched votes Friday did so after reviewing evidence files related to Edward Avery, a former parish priest who in 1999 sexually assaulted a 10-year-old altar boy at St. Jerome Church in Northeast Philadelphia.
Lynn was convicted of endangering that boy because he let Avery remain and celebrate Mass at St. Jerome despite knowing that Avery had molested a boy from St. Philip Neri, in Pennsburg, Montgomery County, in the 1970s.
During the trial, Lynn spent nearly three days on the witness stand arguing that prosecutors had twisted his words and misstated how much power he had. Only Bevilacqua could remove priests, he said.
But when Assistant District Attorney Patrick Blessington lobbed the names of Avery and his victim at the monsignor, Lynn struggled.
His jaw grew tight, his face turned red, and he paused as he searched for answers.
"I did my best with what I could do," was the one Lynn gave at the start of his cross-examination.
"I'm sorry about that," he said days later when Blessington again invoked the boy's name.
"I felt like he was unprepared in a sense," Logan said Saturday. "It didn't sound like he was very clear in his answers at times."
Logan said he didn't think the testimony was decisive in the verdicts. He would not say what persuaded him to vote to convict Lynn.
He said the role and responsibility of other church officials came up almost immediately when deliberations started June 1. More than anything else, he said, the jurors wanted to hear more from or about Bevilacqua, who died in January.
"A lot of us didn't say he deserved blame, but some of us wanted to hear more evidence," Logan said.
He said he did not impose his opinion on other jurors, but rather told them about his own experience in the Army, including two years with a field artillery unit in Korea.
"All I told them was, I'm a soldier, and if my commander tells me to do something that's inhumane or against any kind of Army rules," he would not, Logan said. "I'm a human being before I'm a soldier."
Lynn's lawyers said he stood by his decision to take the witness stand.
"I think this jury needed to hear him," Thomas Bergstrom said minutes after the verdict. "I think, frankly, they were troubled by the fact that this young man got abused. . . . Our position is that he got abused through no fault of [Lynn's]."
His co-counsel, Jeffrey Lindy, repeated their contention that prosecutors erred by charging Lynn with endangerment and that he was being made a scapegoat for the wider failings of church leaders.
"Of course he is," Lindy told reporters. "They had a body there, and the body was Msgr. Lynn."
In the end, jurors did not find evidence that Lynn conspired with Avery and others, or that he had endangered the 14-year boy whom prosecutors say Brennan tried to rape in 1996. Earlier in the trial, the judge had tossed out another conspiracy charge against Lynn and Brennan.
The jurors heard nearly 20 victims testify during the three-month trial. The accounts were wrenching, Logan said, and he said some jurors did not understand why prosecutors called accusers to testify about attacks that occurred years or decades before Lynn became secretary for clergy.
He also acknowledged that a number of jurors agreed that a wrong had been done but had difficulty comprehending and applying the law. At least a third of the 25 questions they sent to the judge during deliberations were requests for clarifications of legal concepts such as conspiracy and endangerment.
"It was a little hard for us," Logan said. "That's why it took so long."
On Monday, Lynn's lawyers are expected to petition Sarmina to let him remain free on house arrest until his Aug. 13 sentencing.
Bergstrom said state sentencing guidelines for a third-degree felony suggested less than a year for someone like Lynn, a 61-year-old with no criminal record and deep ties to the community.
But prosecutors will argue for a much longer term, Blessington told the judge. "Possibly the maximum," he said.
Contact John P. Martin at 215-854-4774, email@example.com, or follow @JPMartinInky on Twitter.
Inquirer staff writer Joseph A. Slobodzian contributed to this article.
We invite you to comment on this story by clicking here. Comments will be moderated.