Wilfredo Flores is seen in Suffolk County Court in Riverhead...

Wilfredo Flores is seen in Suffolk County Court in Riverhead in March 2015. Credit: Joseph D. Sullivan

A Salvadoran immigrant in the country illegally — who pleaded guilty to manslaughter in a deal that limited his sentence to time served — was released from the Suffolk County jail in Riverhead and disappeared for 13 days before immigration agents arrested him to begin deportation proceedings.

The release of Wilfredo Flores set off a scramble among federal authorities, who have prioritized for deportation immigrants in the country illegally who are charged or convicted of serious crimes. He was apprehended on a federal arrest warrant Thursday night, said authorities, who did not reveal where he was captured. A law enforcement source said the search began Wednesday.

It is unclear why agents for U.S. Immigration and Customs Enforcement, which has offices at the Yaphank Correctional Facility just 15 minutes away, did not pick up Flores immediately upon his release.

Although his case was publicized, ICE spokeswoman Rachael Yong Yow said, the agency was never notified of his release.

Michael Sharkey, chief deputy sheriff at the Suffolk County jail, said it was, citing an undated note in Flores’ file.

Flores’ case stands out at a time of aggressive enforcement of immigration laws.

ICE already had shown its interest in the case by issuing what is known as a detainer, or administrative warrant, for Flores, said his attorney, Bryan Browns.

The Suffolk County jail started honoring such detainers at the onset of the Trump administration, when the jail began holding immigrant inmates wanted by ICE for up to 48 hours.

But on Nov. 14, six days after Flores’ plea, a court ruling found that policy “unlawful.” The Appellate Division of the state Supreme Court ruled that state and local law enforcement have no authority to arrest and detain people for civil-law immigration violations.

But there was nothing in the ruling that would block ICE from taking Flores into custody immediately after his release. The justices said they were deciding a narrow issue of whether "state and local law enforcement officers [may] effectuate civil immigration arrests and not whether federal civil immigration officers have the authority to effectuate such arrests."

Flores, now 32, of Bay Shore, was convicted in 2015 of second-degree manslaughter in the stabbing death of Carlos Velasquez, 40, of Central Islip. The two men got into a fight at a party on March 9, 2014, and Flores stabbed Velasquez in the abdomen, slicing his liver and piercing his heart. At trial, Browns argued that Flores was defending himself against the much larger Velasquez.

Last month, a state appellate court threw out the conviction, ruling that a Suffolk prosecutor’s misconduct — going well beyond what the justices said is legally allowed in his closing argument — deprived Flores of a fair trial. On Nov. 8, Flores pleaded guilty to the same crime, but he got a reduced sentence of 1½ to 4 years.

Because he had already served 4 years, 7 months in prison, his sentence was complete. He was not released immediately, however, because jail officials checked with the state prison system to confirm his sentence had been completed. Although that process usually happens quickly, it can take up to two weeks, Sharkey said. Flores was released on Nov. 16.

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