They said in a legal brief that they had “lost faith in Derek Limbocker’s judgment, his management ability, and, most importantly, his integrity.”

Judge Robert E. Gerber denied the request and expressed little sympathy for their plight. At a hearing last month, he said there had been no evidence of criminal conduct and instead portrayed them as overly eager to get their wine when they wanted it.

“What we have instead is a failure to meet predictions, not even promises,” the judge said.

George R. Bunn Jr., a lawyer, wine collector and member of the Bunn coffee maker family, said that Mr. Limbocker, his friend, was the victim of a natural catastrophe. He acknowledged that WineCare’s efforts to get its cellars in order had taken “an awfully long time.”

“Derek is an honest, straight guy,” said Mr. Bunn, who had wine stored at WineCare. “They tell me that 95 percent of the wine should be fine. We all hope we’re not part of the 5 percent.”

A wine enthusiast who once owned a liquor store on the Upper East Side, Mr. Limbocker saw a business opportunity in 2005, when he opened WineCare in the cellars of a brick warehouse that covered an entire block, from 11th to 12th Avenue, between 27th and 28th Streets. He and his partners, including one of the warehouse owners, pitched their service to collectors, restaurants and wine shops.

WineCare featured everything the discerning oenophile would want. Coolers kept the storage cellars at a constant 55 degrees and 60 percent humidity, ideal conditions for preserving old bottles. There was a 24-hour security system and sophisticated software for tracking the location of each bottle.

As rare wine shifted from just a luxurious indulgence to an investment commodity, the company grew rapidly, until October, when the storm sent water gushing into the cellars.