In a motion in Superior Court, Lynn's lawyers say they learned last month that Avery gave prosecutors a statement, and took a polygraph test, in which he denied even knowing the victim, much less assaulting him twice after Masses at St. Jerome Church in Northeast Philadelphia.
If Avery didn't abuse the boy, they argue, then how did Lynn endanger him? "At the very least, knowledge of this information would have affected the tactical decisions" of the defense, Thomas Bergstrom, Allison Khaskelis, and Alan Tauber wrote in their brief.
Tasha Jamerson, a spokeswoman for District Attorney Seth Williams, said the office would have no comment until it filed its response with the court.
The odds for Lynn remain long.
Polygraph results are not admissible in Pennsylvania courts. And Lynn's argument, part of a new motion for bail, requires an appeals court that already denied him bail not only to reconsider that decision, but to wade into an evidentiary issue usually left to the trial judge, who repeatedly rejected other arguments from Lynn.
But the allegation could recast the historic case, and affect others still looming.
One is the trial of another priest, the Rev. Charles Engelhardt, accused of molesting the same boy at the same parish in the 1990s. The other is a civil suit that the accuser, now in his 20s, has filed against Lynn, Avery, and the Archdiocese of Philadelphia.
In many ways, Avery, 70, was the linchpin in the prosecution of Lynn, the former clergy secretary for Cardinal Anthony J. Bevilacqua, who for a dozen years recommended assignments for area priests and was responsible for investigating abuse claims.
When a 28-year-old man told Lynn in 1992 that Avery had molested him as a teen, the clergy secretary had Avery removed from ministry and sent to a church-run hospital for treatment. Lynn also put Avery's name atop a confidential list of area priests he described as "guilty of sexual misconduct with minors."
But in 1995, he recommended that the cardinal return Avery to ministry, and let him live and celebrate Mass at St. Jerome's.
Twice in 1999, prosecutors said, Avery assaulted the altar boy after Masses there, forcing him to dance a striptease and engage in oral sex in a room near the sacristy.
The same boy said he had been previously abused by Engelhardt, a member of a religious order who was living at the rectory, and that Avery mentioned "sessions" with Engelhardt before forcing himself on the boy.
The assertion that two priests abused the same boy in the same church - and knew about each other's misdeeds - was among the most sordid details to emerge in a decade of allegations involving Philadelphia-area priests. It helped draw a national spotlight to a 2011 grand jury report that led to the arrests of Lynn, Avery, Engelhardt, and a fourth accused priest, James Brennan.
But Engelhardt was not a diocesan priest or under Lynn's authority, and he ultimately won a bid for a separate trial. And there was no evidence that Lynn had any prior knowledge of wrongdoing by Brennan. So Avery became critical.
Lynn's lawyers contended that Avery was the lone "mistake" in Lynn's tenure, the only priest ever accused of misconduct after the secretary for clergy had reviewed his case and recommended action.
At the trial, Lynn himself apologized for the attack on the St. Jerome's altar boy, but insisted he had no signs that Avery would re-offend.
Prosecutors said they had evidence that Avery might have molested as many as a half-dozen boys over the decades. But for the plea deal, they required that he admit an attack against just the St. Jerome's altar boy and conspiring with Lynn.
Asked during his hearing by Common Pleas Court Judge M. Teresa Sarmina if he felt he had to plead guilty because he was guilty, Avery paused, then said: "It's something I have discussed and decided to do."
In return he got a prison term that could parole him by age 72.
Avery's plea put Lynn's defense lawyers in a bind. The judge told them that if they tried to challenge the St. Jerome's altar boy on the witness stand, she would let prosecutors tell jurors that Avery had pleaded guilty to the crime. So they declined to cross-examine the accuser.
Bergstrom said Monday that he learned only weeks ago that Avery's lawyers had shared the polygraph results and Avery's denials with prosecutors before negotiating the plea deal. He maintains that it violated court rules that require prosecutors to turn over any material that could help a defendant prove his innocence.
"We all sort of suspected that Avery didn't do it," Bergstrom said Monday. But, he added, "we didn't know he told the commonwealth that."
Contact John P. Martin at 215-854-4774, at email@example.com or follow @JPMartinInky on Twitter.
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