Federal prosecutors handling Mr. Epstein’s sex-trafficking case have said the investigation will not end with his death. In recent lawsuits, his accusers have lodged fresh claims about how they were sexually assaulted on his islands.

In the weeks ahead, the wrangling over Mr. Epstein’s assets is likely to play out on St. Thomas. Last week, lawyers handling Mr. Epstein’s estate filed his will in court on St. Thomas and said he had more than $570 million in assets.

Mr. Epstein arrived in the Virgin Islands in 1998, when he paid $7.95 million for Little St. James, a roughly 70-acre island. Mr. Epstein called it “Little St. Jeff’s.” In 2016, he bought the larger Great St. James for $17.5 million.

Over the years, he spent millions more developing the islands, including building a villa with a library, a Japanese bathhouse and a movie theater.

His construction projects led to repeated clashes between Mr. Epstein and the Virgin Islands Department of Planning and Natural Resources, according to paperwork related to his work permits reviewed by The New York Times.

A memo from the agency’s wildlife chief in 2010 noted that Mr. Epstein’s properties had “a long history of egregious and blatant disregard for environmental regulations.” Projects had “introduced several nonnative species to the island.” The arrival of one invasive species, the Cuban tree frog, led to a recommendation that all landscaping and building materials be inspected, the memo said.