Earlier this year, the lab shelved the two methods and replaced them with newer, more broadly used technology.

A coalition of defense lawyers is asking the New York State inspector general’s office — the designated watchdog for the state’s crime labs — to launch an inquiry into the use of the disputed analysis methods in thousands of criminal cases. While the inspector general has no jurisdiction over the court system, any finding of flaws with the DNA analysis could prompt an avalanche of litigation. Previous convictions could be revisited if the flawed evidence can be shown to have made a difference in the outcome.

The medical examiner’s office “has engaged in negligent conduct that undermines the integrity of its forensic DNA testing and analysis,” the Legal Aid Society and the Federal Defenders of New York wrote the inspector general on Friday. Because the lab has kept problems with its “unreliable” testing and “unsound statistical evidence” secret from the public and the courts, they continued, “innocent people may be wrongly convicted, and people guilty of serious crimes may go free.”

In addition to those convicted using the disputed methods, many defendants may have chosen to plead guilty when they learned prosecutors had DNA evidence against them. Their cases face significant barriers to reconsideration.

The medical examiner’s office stands by its science. Its chief of laboratories, Timothy Kupferschmid, said that the discarded techniques were well-tested and valid, and that the lab was adopting newer methods to align with changing F.B.I. standards. He compared it to a vehicle upgrade.