For years, the main challenge facing West End Temple — an approximately 90-family Reform congregation in the Neponsit section of Rockaway, Queens — was demographics.

Now, the struggle to thrive amid an aging and shrinking non-Orthodox population seems minor compared to repairing over $1 million in damages caused by four feet of floodwater.

While the Union for Reform Judaism is helping raise money for the temple, UJA-Federation of New York is offering assistance and other congregations are mobilizing volunteers to help, Rabbi Marjorie Slome — like leaders of other institutions hit hard by Sandy — is also hoping for financial help from the Federal Emergency Management Agency (FEMA).

“I am a separation of church and state kind of person, but if my temple were to have a fire, the Fire Department is not going to pull up and say this is a synagogue, we can’t put out the fire; our garbage gets picked up by the New York Department of Sanitation,” Rabbi Slome. “I’m hoping FEMA will step forward.”

In a move that could help West End, as well as other synagogues and religious institutions damaged in Hurricane Sandy — and that some church-state watchdogs fear could weaken the Establishment Clause — the Orthodox Union is seeking to make houses of worship eligible for FEMA grants.

Currently, FEMA provides grants to a variety of nonprofits, but not houses of worship. The OU, which in 2001 successfully persuaded the U.S. Department of Justice’s Office of Legal Counsel to include parochial schools in the list of nonprofit organizations eligible for FEMA disaster relief grants and has been instrumental in obtaining government funds to protect Jewish institutions from potential terrorist attacks, is currently in discussions with officials at the Department of Homeland Security (under which FEMA operates) to add houses of worship to the list of FEMA-eligible nonprofits.

In a memo issued Tuesday to synagogue leaders in Sandy-impacted communities, Nathan Diament, the OU’s executive director for public policy, said, “We are making progress, but the discussions are ongoing.” In the meantime, the OU, UJA-Federation of New York and Jewish Community Relations Council of New York are encouraging synagogues to begin preparing applications, which must be filed by Nov. 29.

Just how much aid could be available remains to be seen, as FEMA’s budget — like that of most federal agencies — is subject to the “fiscal cliff” spending cuts currently being negotiated in Congress.

However, with Adina Frydman, director of UJA-Federation’s Synergy department, reporting that at least 45 area synagogues “sustained some damage” in Hurricane Sandy, including approximately 10 that are now “uninhabitable,” FEMA grants could provide a welcome boost to congregations struggling to pay for any repairs not covered by their insurance plans.

“Not all synagogues have insurance, and even if they do, they don’t all have flood insurance,” Frydman said, adding that flood insurance tends to have “very high deductibles.”

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Whereas two decades ago, Supreme Court interpretations of the U.S. Constitution’s Establishment Clause “were on the side of saying government cannot give money to a parochial institution even for reconstruction in the wake of a disaster,” the situation has gradually shifted to a climate more sympathetic for faith-based groups, the OU’s Diament told The Jewish Week. Now, “if the government is providing funding to a broad group of institutions due to circumstances and criteria that have nothing to do with religion, that’s not a church-state problem anymore.”

In 2002, after the Seattle Hebrew Academy was damaged in an earthquake and initially denied FEMA aid, the OU helped the school appeal that decision, persuading the OLC to issue a memo authorizing FEMA to assist the school.

That memo concludes that direct disaster-relief aid to parochial schools is constitutional “where made available on the basis of genuinely neutral criteria, to an array of beneficiaries including both educational and non-educational institutions. Indeed, there are arguments that excluding religious organizations from disaster assistance made available to similarly situated secular institutions would violate the Free Exercise Clause and the Free Speech Clause.”

To ensure that Seattle Hebrew Academy would not simply be a onetime exception, in 2007 the OU successfully got the statute that governs FEMA amended “to explicitly make it clear that non-public, nonprofit schools are eligible for disaster reconstruction funds,” Diament said. “It’s very clear in the law that schools are eligible. The open question at the moment is with regard to houses of worship, which are not explicitly mentioned in the statute.”

That same year, Diament said, the OLC put out a memo “explaining that when the government gives out grants for historic preservation of buildings, landmarked religious buildings can receive those funds as well.”

The Union for Reform Judaism and its Religious Action Center, which generally oppose government funding for religious groups, has not made any public statements about whether FEMA aid poses a church-state conflict. However, it has shared FEMA application information with its member synagogues and cooperated with the OU and UJA-Federation in efforts to gather information about the extent of synagogue damages. Neither URJ President Rabbi Rick Jacobs nor RAC Executive Director David Saperstein was available for comment.

Told about the effort to make houses of worship eligible for FEMA grants, Alex Luchenitser, associate legal director of Americans United for Separation of Church and State, said, “This raises very serious constitutional issues and also raises difficult questions.”

“We realize there’s a lot of people that need help out there,” he said. “But we are also concerned that this tragedy not be used to erode the U.S. Constitution and the wall of separation between church and state to direct taxpayer-funded dollars to religious institutions.”

While he sees no issue in including houses of worship among those “receiving direct services” from federal disaster-relief personnel, Luchenitser said that grants are more problematic.

“It could open the door to funds going to religious organizations in other contexts where you don’t have a disaster,” he said.

Asked how this would differ from Homeland Security’s existing grant allocations to synagogues to help protect them from terrorist attacks, he said, “It’s one thing to protect people at high risk of being subject to terrorist attacks, because you’re protecting individuals rather than supporting religious activity. But if you’re talking about grants to rebuild a church or synagogue, then you’re talking about taxpayer money being used to build a facility used for religious worship.”

Asked if his group would do anything to challenge house-of-worship eligibility for FEMA, Luchenitser said, “It’s premature to discuss.”

In choosing which synagogues to damage, Hurricane Sandy apparently took a pluralistic approach.

Frydman of UJA-Federation’s synagogues department, said the congregations sustaining the most serious damage hail from all denominations: for example, in the Rockaways, Oheb Zedek is Orthodox, Temple Beth El is Conservative and West End Temple is Reform.

Most of the synagogue damage has been from flooding, with salt water corroding “pretty much everything” and health risks posed by mold. In addition, some synagogues suffered “tree damages,” while others, still without power, have been unable “to go in and assess the extent of the damage,” Frydman said.

The federation does not “want to replace government dollars” in its assistance to Sandy-affected synagogues, but is currently helping in a variety of other ways, Frydman said, including providing congregations in Zone A and on the South Shore with $5,000 for their rabbis’ discretionary funds and matching damaged synagogues with undamaged congregations that are eager to help.

A Synergy staff member is working full time right now to help synagogues dispatch volunteers to congregations in need, both for onetime efforts and those synagogues that “want to twin with or adopt another synagogue.”

“There’s been a tremendous outpouring from synagogues in a position to help,” she said, among them Temple Israel on the Upper East Side, Congregation B’nai Jeshurun on the Upper West Side, Dix Hills Jewish Center and Brooklyn’s Congregation Beth Elohim.

“One of the things I’ve been most impressed with is how synagogues have opened their doors,” she said, citing many that have shared their space with other institutions and have invited individuals in for food, electricity and WiFi.

“All the old turf issues have gone out the window, which is really, really nice,” she said, adding, “It sends a very strong statement about the relevance of synagogues in people’s lives and their centrality as an important hub of community.”

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