His stay in sanctuary was among the longest, but given that President Barack Obama also made extensive use of deportations, there are two other people still taking refuge after more than a year and a half. At the other end of the spectrum, Mr. Andersen said, one woman from Guatemala who took refuge in July in a Pentecostal church in New Haven had her immigration case resolved in less than a week.

This week, churches in Raleigh, N.C.; Meriden, Conn.; and Highland Park, N.J., announced that they were offering sanctuary to a total of four people. The New Jersey church took in a couple who say they could face persecution for their Christian faith if they were deported back to Indonesia. It is their second time in sanctuary in the same church, according to the pastor, Seth Kaper-Dale, an immigration activist who is now running for governor on the Green Party ticket.

It is the policy of the Immigration and Customs Enforcement agency that churches, schools and hospitals are “sensitive locations” where immigration officers are not supposed to make arrests except in extraordinary circumstances.

So far, the “sensitive locations enforcement policy has not changed” under President Trump, said Jennifer Elzea, the agency’s acting press secretary: “I’ve not been aware of any instances in which we’ve entered a church or place of worship to conduct enforcement actions.”

Mr. Flores took sanctuary last November at the Arch Street United Methodist Church, one day before he was supposed to report for deportation back to Mexico. He had been living in the United States on and off since 1997, and had been caught nine times trying to cross the border illegally, immigration officials said. Mr. Flores said he had compelling reasons for doing so: A longtime partner, Alma Lopez, their two sons, and Ms. Lopez’s teenage daughter, whom he considers his stepdaughter, all lived in the United States. Mr. Flores supported them by working as an arborist.

“I’ve never brought drugs, I’ve never helped anybody else cross the border — my only crime is coming back,” Mr. Flores said in an interview in the church last December. “I came here for the love of my children.”