JPMorgan Chase & Co. has been cleared of wrongdoing after an institutional investor (Christ Church Cathedral of Indianapolis) sued the bank last year, for selecting “unsuitable and poorly performing investments” including structured notes, causing the church trusts to lose $13m in value from July 2004 to December 2013.

US District Judge Larry McKinney in Indianapolis on 21 May rejected the case against JP Morgan and gave the Episcopal church a month to refile two of its claims, although a breach of trust claim lodged against JP Morgan Chase Bank NA unit, for which dismissal wasn’t sought, remains.

The judge said church lawyers had lumped together multiple JPMorgan units as to “nearly all allegations” in its court papers and said their allegations lacked specificity, and that it is impossible to tell which entity owes any duty to the church and which entity was specifically involved in alleged self-dealing or made misrepresentations or omission.

JPMorgan put 68% to 85% of the church’s assets into its own products, including private equity funds, structured notes and hedge funds, according to the complaint, including its Highbridge Dynamic Commodities Strategy Fund, which lost 17% over its lifetime before folding last year; 88 structured notes; nine off-shore hedge funds all created by the bank; two off-shore private equity funds committing $1m of trust funds; two losing hedge funds sold by a JP Morgan subsidiary, Highbridge Capital Management; and twenty-five other proprietary mutual funds including funds.

The bank and the notes’ issuers may have charged fees of up to 11% of their value during the time they were in the trust while the church’s return on the notes, after fees, averaged 1.4% annually over six years through December 2013, according to the law suit.

Court papers stated that, when JPMorgan took over the church’s trust fund in the summer of 2004, it had $34.6m but the value of the fund fell to $31.6m by December 2013, preventing the church from doing some of its charitable work around a food bank, a homeless shelter and a centre of abused women.

The church claims that by 2007, JPMorgan started adding alternative investments including structured notes, derivatives and hedge funds, for which the church had to pay over five times more in management fees, which raised to $177,800 by 2013 from $35,000 a year in 2004, as well as other fees that the bank never fully disclosed those despite repeated requests from the church, alleges the lawsuit which also shows that by the end of 2009, JPMorgan had the church invested in 52 different investment funds, with 75% of them in JPMorgan’s own proprietary products.

The lender denied wrongdoing, saying in an October 2014 court filing that Christ Church Cathedral “painted a grossly inaccurate picture” of how its trusts were managed.

“Contrary to the church’s allegations of fraud and mismanagement, the bank achieved positive returns for the trusts through one of the worst financial crises in U.S. history,” the bank said in court papers adding that even though the Trust distributed more than $13m to the church between 2006 and 2013, the trust still gained well over $10m during that period.

JP Morgan stepped down as Christ Church Cathedral’s trustee a year ago. In an October court filing, it sought to dismiss the suit, saying the church didn’t have the standing to file a securities claim in part because it didn’t buy or sell securities, and that the allegations weren’t specific enough.

In February, Christ Church Cathedral dropped a federal securities-fraud claim and a claim for breach of fiduciary duty, after the New York-based bank asked the court to strike the latter as redundant.

Pence Hensel, the law firm representing the church, will file an amended complaint which will establish that JPMorgan was more interested in its own financial interests to the detriment of Christ Church, said a spokesperson at the law firm.

A JP Morgan spokesperson declined to comment on this case.

The case is Rector, Wardens and Vestrymen of Christ Church Cathedral of Indianapolis v. JPMorgan Chase and Co., 14-cv-01331, U.S. District Court, Southern District of Indiana (Indianapolis).

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