In a court filing on Tuesday, prosecutors said some of the funds Mr. Zuberi donated to the inaugural committee came from other people, including an unnamed American man who wrote a $50,000 check to Avenue Ventures to secure “exclusive access to certain inaugural events” promised by Mr. Zuberi.

The man, who is not identified in the filing, did not attend the inauguration, and asked Mr. Zuberi to refund the $50,000, according to the prosecutors from the United States Attorney’s Office for the Southern District of New York. They said in the filing that Mr. Zuberi initially declined to refund the money. He relented, they said, only after The New York Times and other news media outlets reported in early February 2019 that Mr. Zuberi’s name and that of his company were included on a subpoena for documents sent to Mr. Trump’s inaugural committee as part of a wide-ranging investigation into the inauguration and its financing.

At a meeting at a restaurant in California a few weeks after the news broke, Mr. Zuberi asked the man whether he had been contacted by federal investigators, according to the prosecutors. They wrote that Mr. Zuberi wrote a refund check to the man, backdating it to Feb. 1 “to make it appear” that Mr. Zuberi returned the money “before he learned of the S.D.N.Y. investigation into the source of funds for the $900,000” donation.

The prosecutors also accused Mr. Zuberi of deleting emails with individuals who provided money to him around the time of his $900,000 donation, including a foreign citizen. The foreigner, who is not named in the court filing, transferred approximately $5.8 million to the account Mr. Zuberi used to fund his $900,000 inaugural donation, the prosecutors said.

When prosecutors confronted Mr. Zuberi’s lawyers about his efforts to delete emails with the foreigner, Mr. Zuberi contacted his email service provider seeking advice on “how to ensure that copies of his emails were not stored on a server,” according to the filing.