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NEW YORK — There will soon be a rooftop swimming pool where the copper-domed bell towers of Mary Help of Christians once rose.

Formerly a hub of the East Village’s Italian-American community, the site of the Roman Catholic Church is now slated for a 158-unit rental building, complete with basement gym and rooftop gardens — a familiar trajectory for a growing number of houses of worship as church attendance falls and real-estate values soar.

In the rubble-strewn lot on Avenue A between 11th and 12th Streets where Mary Help of Christians and its school and rectory long stood, a rusty basketball hoop and strip of blacktop are all that is left.

But perhaps unknown to those mourning the church’s passing, much of what was precious inside it — and other now-closed Catholic churches — sits in a Staten Island warehouse, awaiting a second chance.

At the warehouse are the rows of papier-mâché statues of saints that once flanked the pews at Mary Help of Christians, their brightly painted faces peering out from cloaks of packaging material.

Nearby, wood and tin organ pipes are stacked like torpedoes. There are jumbles of votive stands and thickets of chandeliers, dismantled Carrara marble railings and quarter-ton church bells.

Some items ended up at the warehouse after the 2007 decision of the Archdiocese of New York to close or shrink 21 parishes. Others came because of renovations. Much more will be coming; the archdiocese plans to announce another round of parish closings in 2014.

The archdiocese has not always had an organized system for dealing with vestments, patens, candle-drip guards and myriad other ritual objects when they are no longer needed. Before 2004, some ended up in antique stores or trash cans while others went to parishioners or other churches.

Then there was realization that “these things, even if they don’t have great financial value, have historical value, or liturgical value, and we should preserve them,” said Joseph Zwilling, a spokesman for the archdiocese.

Kevin Shaughnessy, the 62-year-old facilities manager, who was chosen in 2004 to organize the diocese’s patrimony, told another story. He had heard a legend that his job was born after a bishop spotted on a barroom shelf an artifact from the church where he had started his priesthood. The next thing he knew, “Tag, I was it,” Shaughnessy said.

Shaughnessy fashioned the warehouse from a decaying, former dormitory for abused children at the Mission of the Immaculate Conception in Mount Loretto. He spends his days there mostly alone, carefully storing relics by type.

Stained glass is protected by plywood frames, and organ consoles are put together in a corner. A shelf gleams with brass chalices and ciboria. Tiny medals with pictures of saints are tucked into one of his old pill bottles.

“I’m a product of a Depression-era family,” he said. “I was always taught to find a use for everything.”

Detailed catalogs list the contents that have come from each church, as well as their value.

The methodical approach is to help priests and their architects, who are invited to come to the warehouse to purchase objects for their parishes at a fraction of their appraised worth. Sales to laypeople — even lay church members — are not allowed.

In 2007, the archdiocese said it would not sell closing churches to developers, but that turned out not to be the case.

Mary Help of Christians was sold in December 2012 to Steiner NYC for $41 million. Near the Holland Tunnel, Our Lady of Vilnius, a former Lithuanian Church, was put on the market by the diocese for $13 million.

It sold in October to the Extell Development, which is flipping the property and asking $19 million for it. A brochure suggests 22 stories of apartments could be built there.

In 2012, Artimus Construction, a major developer of residential buildings in gentrifying Harlem, purchased St. Thomas the Apostle, a massive neo-Gothic confection on West 118th Street that had sat vacant since 2003. Items, including stone angels and the sink from its sacristy, are now arriving at Shaughnessy’s domain; apartments are also reportedly planned at that site.

Shaughnessy said his next big job is to salvage objects from the Church of St. Vincent de Paul at 123 W. 23rd St. It is another of the churches whose closing was announced in 2007, but its largely French- and Creole-speaking parishioners fought for years to save it.

The archdiocese now has an offer on the property and is awaiting Vatican approval for the sale, Zwilling said. Many of the church’s liturgical objects will follow worshippers to their new parishes, but some will end up at the warehouse to await adoption.

Much does get reused. A priest from the Church of St. Lawrence O’Toole in Brewster, N.Y., an expanding parish, was coming to shop for vestments and artwork, Shaughnessy said.

A Staten Island parish near a police station now hosts a statue of St. Michael the Archangel, the patron saint of police officers, from Mary Help of Christians.

The renovated altar at Holy Cross Church on West 42nd Street came from a shrine at St. Ann’s Church on East 12th Street. That church was torn down in 2005, though the facade was preserved and now sits, like a stage set, in front of a 26-story New York University dormitory.

Other objects, out of use or fashion, will likely be stored for the long haul, including several brass vessels that hold both wine and the sacred host for Mass (they must be separate vessels now) and the large, black-and-gold bas reliefs that decorated a Brutalist style, mostly concrete chapel on Washington Square Park before it was sold to New York University and demolished.

The bas reliefs are made of painted plastic foam, and their angular aesthetic is part space-age, part 1970s. One depicts Mary pregnant with Jesus, his form evident in the hollow of her abdomen.

“Chances are, when all of us die and go to heaven, that will still be sitting there,” Shaughnessy said.