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A second member of the Harvey Weinstein prosecution team quit the Manhattan DA’s Office last month amid controversy over whether the lead investigator — or lead prosecutor — covered up damaging evidence against an accuser, The Post has learned.

Veteran prosecutor Jennifer Gaffney, deputy chief of the Sex Crimes Unit, was thrown a going-away party on Sept. 20, sources said Monday.

Her party took place just one day before ADA Rachel Hochhauser, who was “second chair” on the Weinstein trial team, also departed the DA’s Office for a job at a private investigations and security firm.

It was unclear whether Gaffney — whose husband, Christopher Schmidt is an NYPD lieutenant — quit to start a new job.

Gaffney, 45, declined comment outside her home Monday.

According to news releases issued by Manhattan DA Cyrus Vance Jr. over the summer, Gaffney and Hochauser comprised half of the four-member team prosecuting Weinstein, the disgraced co-founder of a movie empire with his brother Bob.

Both Gaffney and Hochhauser left the DA’s Office around the time lead prosecutor Joan Illuzzi-Orbon wrote a Sept. 12 letter to the defense alleging that NYPD Det. Nicholas DiGaudio had admitted withholding information from a witness he interviewed in February.

According to Illuzzi-Orbon’s letter, the unidentified woman told prosecutors that Lucia Evans — who has accused Weinstein of forcing himself on her in 2014 — confided that she performed oral sex on Weinstein after he offered to get her an acting job, the letter says.

DiGaudio claims he informed Illuzzi-Orbon about the Evans snafu and that a fellow cop was present at the time, said law enforcement sources.

Last week, prosecutors dropped the Evans third of the case, leaving intact allegations that he raped another woman and sexually assaulted a a third.

Weinstein lawyer Benjamin Brafman said he would now seek to have the entire case thrown out based on the allegations against DiGaudio.

Vance spokesman Danny Frost said Gaffney’s resignation — which she submitted July 27, effective Sept. 7 — had nothing to do with the Weinstein case.

Hochhauser and Gaffney were both replaced by ADA Brendan Tracy of the Sex Crimes Unit, Frost said.

Additional reporting by Kenneth Garger