A year after its principal was removed amid an investigation into cheating fraud, the middle school at Choir Academy of Harlem saw its city evaluation tumble.

In falling from a B in 2011 to a F this year, Choir Academy was one of 10 schools to see its progress report grade drop by three letter grades, a jarring change in a year when city officials touted the relative year-to-year stability of its progress reports.

Update: The city released a shortlist of schools it would consider closing this afternoon. Choir Academy was not on the list. The school was included on the city’s second list, which was released days later.

Parents and staff at the troubled school said on Monday that Choir Academy is back on track this year because it has a new principal. Melissa Vaughan abruptly replaced Andrea Ellen Parris in January when Parris was denied tenure after four years at the school.

Under Parris, the school significantly improved its graduation rate and test scores, but a department spokeswoman said today that investigators had spent most of the last two years looking into allegations of cheating.

Choir Academy’s high school was a rare success story to emerge from the city’s thwarted attempt to close 19 schools in 2010.  A judge reversed the closure plan on a technicality, but the city ended up closing most of those schools a year later.

But Choir Academy stayed open. Given the extra school year, graduation rate climbed by 12 percentage points, thanks mainly to summer school credit accumulation. The school started showing large gains in its middle school grades as well.

Yet at the same time, two separate investigations were opened in response to allegations, said Connie Pankratz.

Officials were unable to verify either allegation, Pankratz said. But the city denied tenure to Parris in December and she did not return to Choir Academy after the Winter Recess. In January, investigators closed the second cheating case.

In April, monitors visited during the state exam period and scrutinized the school’s test security practices  after the department raised red flags about the school’s significantly improved test scores.

After the visit, math proficiency on the tests fell by 50 percent, just one year after they improved by 75 percent. Graduation dropped from 72 percent to 67 percent.

Efforts to reach Parris this week were unsuccessful.

A school aide said Monday that under Vaughan’s leadership, the school had seen a “complete turnaround. It’s another atmosphere. Everything’s different.”

Vaughan declined to comment.