WASHINGTON — A lawyer for President Trump broached the idea of Mr. Trump’s pardoning two of his former top advisers, Michael T. Flynn and Paul Manafort, with their lawyers last year, according to three people with knowledge of the discussions.

The discussions came as the special counsel was building cases against both men, and they raise questions about whether the lawyer, John Dowd, who resigned last week, was offering pardons to influence their decisions about whether to plead guilty and cooperate in the investigation.

The talks suggest that Mr. Trump’s lawyers were concerned about what Mr. Flynn and Mr. Manafort might reveal were they to cut a deal with the special counsel, Robert S. Mueller III, in exchange for leniency. Mr. Mueller’s team could investigate the prospect that Mr. Dowd made pardon offers to thwart the inquiry, although legal experts are divided about whether such offers might constitute obstruction of justice.

Mr. Dowd’s conversation with Mr. Flynn’s lawyer, Robert K. Kelner, occurred sometime after Mr. Dowd took over last summer as the president’s personal lawyer, at a time when a grand jury was hearing evidence against Mr. Flynn on a range of potential crimes. Mr. Flynn, who served as Mr. Trump’s first national security adviser, agreed in late November to cooperate with the special counsel’s investigation. He pleaded guilty in December to lying to the F.B.I. about his conversations with the Russian ambassador and received favorable sentencing terms.