He will assist Flanagan - the Orioles' executive vice president of day-to-day operations - in day-to-day aspects of the position, including salary negotiations, arbitration and player personnel decisions.
The 39-year-old Duquette was named the Mets' interim general manager on June 12, 2003 after the firing of Steve Phillips, and was officially named the club's 10th general manager on Oct. 28, 2003.
However, when Minaya left the Montreal Expos organization for the same position with the Mets in September 2004, Duquette was abruptly removed from the position.
Duquette served as the Mets' senior vice president of baseball operations - a secondary role underneath Minaya - in 2005, but spoke for the club on a number of occasions and represented team administration on road trips.
The Philadelphia Phillies fired general manager Ed Wade after the season and have been reported to show mild interest in Duquette, but it is believed they are waiting to see if Brian Cashman leaves the Yankees.