Assistant District Attorney Joan Illuzzi-Orbon said the complainant was told by a detective to “delete anything she did not want anyone to see”.
Harvey Weinstein’s lawyer said the development “undermines” the case.
He faces charges involving alleged assaults on two women. The Hollywood producer denies the charges.
Joan Illuzzi-Orbon wrote in a letter to Harvey Weinstein’s lawyer, Ben Brafman: “My office had asked Complainant 2 to produce any and all cell phones that she might have used during the time she interacted with the defendant.”
However, she adds that the woman said she was then advised to remove files “before providing the phones to our office”.
Despite this advice, the woman still provided the phones used to communicate with Harvey Weinstein “without any deletions”, Joan Illuzzi-Orbon said.
Ben Brafman later released a statement in response to the letter, saying the news “further undermines the integrity of an already deeply flawed indictment of Mr. Weinstein”.
The lawyer earlier requested that the entire case be dismissed.
Last week a charge against Harvey Weinstein by actress Lucia Evans was dismissed by a judge in New York after she was said to have given a differing account of events.
Hervey Weinstein has been accused of assault by more than 70 women.
The accusations against the producer helped awaken the #MeToo movement, which has seen hundreds of women accusing high-profile men in business, government and entertainment of sexual abuse and harassment.
Harvey Weinstein, 66, has agreed to wear a GPS tracker and to surrender his passport.
The film mogul also faces additional investigations in Los Angeles and London, and by the US federal government.
Harvey Weinstein, who has been on $1 million bail since his arrest in May, denies having non-consensual contacts, his lawyers have previously said.
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