"It is beyond doubt that Msgr. Lynn was completely unaware of this act of obstruction," attorneys Jeffrey Lindy and Thomas Bergstrom wrote.
Their motion asks Common Pleas Court Judge M. Teresa Sarmina to dismiss the conspiracy and endangerment charges against Lynn, or to bar prosecutors from introducing Bevilacqua's videotaped testimony at trial.
The cardinal died Jan. 31.
The revelation is likely to further cloud Bevilacqua's complicated legacy in the handling of clergy sex abuse and could shape what happens at the historic trial, the first for a cleric accused of covering up sex abuse. Jury selection began this week. Opening statements are March 26.
Prosecutors say that Lynn, as the secretary for clergy, recommended priests for assignments despite knowing or suspecting that they would sexually abuse children. Facing trial with him are two former parish priests accused of molesting a boy in the 1990s, the Rev. James J. Brennan and Edward Avery.
In their motion, Lynn's lawyers argue that the new documents show he was one of the few church officials trying to confront the issue of abuse.
After becoming secretary for clergy in 1992, they say, Lynn began combing the secret personnel files of hundreds of priests to gauge the scope of misconduct involving children. He did it, his lawyers said, because he "felt it was the right thing to do."
The result was his February 1994 memo that identified 35 priests suspected of abuse or pedophilia. Lynn allegedly gave it to his superior, Msgr. James Molloy, the assistant vicar for administration, who shared his duties documenting abuse complaints.
Bevilacqua discussed the memo in a March 15, 1994, meeting with Molloy and Bishop Edward P. Cullen, then the cardinal's top aide, the filing says. After the meeting, Bevilacqua allegedly ordered Molloy to shred the memo.
One week later, Molloy allegedly destroyed four copies, with the Rev. Joseph Cistone as a witness. "This action was taken on the basis of a directive I received from Cardinal Bevilacqua," say Molloy's handwritten notes.
But Molloy apparently had second thoughts. Without telling anyone, he took a copy of the memo, and his notes, and placed them in a portable, locked safe.
According to the motion, that safe remained untouched and unnoticed until 2006, when archdiocesan officials found it and hired a locksmith to open it. It's unclear why the records inside were only recently turned over to Lynn's lawyers and prosecutors, although church lawyers have said they have been reviewing thousands of files to comply with trial subpoenas.
Bevilacqua had cited the 35 priests before. In February 2002 - as the abuse scandal was roiling Catholics across the country - he said the archdiocese had turned over information on 35 suspected abusive priests to the Philadelphia District Attorney's Office. He did not mention any memo from eight years earlier or his order to shred it.
During 10 appearances before a grand jury in 2003 and 2004, Bevilacqua denied knowing details or playing a significant role in the handling of sex-abuse complaints, saying he delegated those duties to Lynn.
"I saw no evidence at any time that we did any cover-up," he testified.
Prosecutors have not disputed that a conspiracy to protect abusive priests stretched beyond Lynn. Last month, one assistant district attorney called the archdiocese "an unindicted coconspirator" in the case.
Lynn's lawyers argue that Bevilacqua's testimony may have been perjury and that it colors the current case. "Had this recent grand jury been aware of the cardinal's successful efforts in 'deep-sixing' a significant document prepared by Msgr. Lynn, its view of him as a potential defendant may have been entirely different," they wrote. "It is clear . . . that Msgr. Lynn has been 'hung out to dry.' "
Lynn's lawyers also contend that Cistone, now the bishop of Saginaw, Mich., and Cullen, the retired bishop of Allentown, misled the grand jury by not acknowledging the memo or the cardinal's order to shred it. Neither responded Friday to messages left at their dioceses.
Molloy left his post as an administrator in the mid-1990s and died in 2006, after the first grand jury report vilifying the archdiocese. He never openly discussed Lynn's 1994 memo, but might have foreshadowed it in a story published after his death.
In an interview with the National Catholic Reporter, Molloy described reaching a point when "I couldn't be sure that I could trust my superiors to do the right thing." So, he said, he became diligent about documenting his actions.
"I wanted my memos to be there if the archdiocese's decisions were eventually put on the judicial scales," Molloy said then. "This way, anyone could come along in the future and say, this was right or this wrong. But they could never say it wasn't all written down."
Contact staff writer John P. Martin at 215-854-4774,
@JPMartinInky on Twitter.