In recent years, plea bargains of all sorts have dominated the criminal-justice system: They now account for almost 95 percent of the final dispositions in felony cases across the nation. Even the Supreme Court has acknowledged their pre-eminence, writing in 2012 that “criminal justice today is for the most part a system of pleas, not a system of trials.”

Alford pleas, however, are exceptionally rare, composing only 6 percent of all the guilty pleas in state and federal courts, according to a study published in 2009. While some legal experts have assailed them as a patent violation of due-process rights, others have described them as a psychological salve: They allow defendants to maintain their innocence even as they bow to the reality that they would likely be convicted at a trial.

But then there are defendants like Mr. Harris, who entered his plea decades after his conviction and only, as he put it, “under duress.” Across the country, different prosecutorial agencies take different positions when facing cases that might be marred by a wrongful conviction. Some, like the Brooklyn district attorney’s office, have decided that the most just option is simply to reverse a bad conviction and wipe a defendant’s slate entirely clean. But others use guilty pleas and sentence modifications to free people from prison in dubious prosecutions.

In Mr. Harris’s case, the prosecutor who tried the matter had not disclosed exculpatory evidence. Scientific testing also showed that DNA on the victim’s clothes could not have come from him. The victim failed at first to pick out Mr. Harris in a photograph array, but then, at trial, identified him for the first time as the man who had attacked her. Earlier this year, a Connecticut judge made it impossible to rely on her testimony, ruling that prosecutors could no longer use witnesses whose sole identification of a suspect came in court.

Legal experts say that even if defendants who enter guilty pleas are eventually released, they are often subject to collateral effects that could include losing government benefits or the legal right to vote. The strategy of hinging a release on entering a plea also allows a prosecutor’s office to keep a guilty finding on its records and thus avoid being sued.