Another former principal, Lionel Rubio, said he knew of six students who had been pushed out of high school and had not pursued an education since. In 2008, Linda Hernandez-Romero’s daughter repeated her freshman year at Bowie High School after administrators told her she was not allowed to return as a sophomore. Ms. Hernandez-Romero said administrators told her that her daughter was not doing well academically and was not likely to perform well on the test.

Ms. Hernandez-Romero protested the decision, but she said her daughter never followed through with her education, never received a diploma or a G.E.D. and now, at age 21, has three children, is jobless and survives on welfare.

“Her decisions have been very negative after this,” her mother said. “She always tells me: ‘Mom, I got kicked out of school because I wasn’t smart. I guess I’m not, Mom, look at me.’ There’s not a way of expressing how bad it feels, because it’s so bad. Seeing one of your children fail and knowing that it was not all her doing is worse.”

The program was known as “the Bowie model,” and Mr. Garcia had boasted of his success in raising test scores, particularly in 2008, when all of the district’s eligible campuses earned a rating of “academically acceptable” or better from the state. But parents and students had another name for what was happening: “los desaparecidos,” or the disappeared.

State education data showed that 381 students were enrolled as freshmen at Bowie in the fall of 2007. The following fall, the sophomore class was 170 students. Dozens of the missing students had “disappeared” through Mr. Garcia’s program, said Eliot Shapleigh, a lawyer and former state senator who began his own investigation into testing misconduct and was credited with bringing the case to light. Mr. Shapleigh said he believed that hundreds of students were affected and that district leaders had failed to do enough to locate and help them.

“Desaparecidos is by far the worst education scandal in the country,” Mr. Shapleigh said. “In Atlanta, the students were helped on tests by teachers. The next day, the students were in class. Here, the students were disappeared right out of the classroom.”

Image Lorenzo Garcia, the ex-superintendent. Credit... Ruben R Ramirez/EL PASO TIMES, via Associated Press

Court documents list six unindicted co-conspirators who assisted Mr. Garcia, but they have not been publicly identified. Parents and educators believe that several of those involved in the scandal continue to work in the system or have taken jobs at nearby districts. The El Paso district, meanwhile, has had trouble maintaining its leadership, with the board of trustees appointing three interim superintendents since Mr. Garcia’s arrest last year.