Boeheim said Flynn's status is "kind of up in the air."
Last week the school announced that all three players planned to make themselves eligible for the draft.
The coach said Devendorf and Harris are virtual locks to leave, but Flynn might still opt to come back to school.
Flynn led the team in scoring at 17.4 points per game and set an Orange record by playing 1,418 minutes in his sophomore year. After two seasons, he ranks seventh in career assists (439) at Syracuse.
He indicated he will not hire an agent, giving him the option to return to school.