Emerson, who went missing at one stage last season, was given permission by Robson to return home during a two-match suspension, but he was expected back for the game against Stockport.
"We got a telephone call yesterday saying that Emerson had not got on a plane to arrive back in England. I don't know any more than that," Boro's manager, Bryan Robson, said. "I'll speak to him and try to find out his reasons. Emerson seemed to be happy at the club and there have been no explanations from him. Emerson is just another player and these things happen within clubs. Until I speak to him, I cannot say any more."
Craig Hignett put Boro ahead after Eric Nixon failed to hold a Phil Stamp shot, but Stockport hit back when Flynn headed home Tom Bennett's corner. Boro failed to find their rhythm at the start of the second-half, but went ahead when Nixon could only parry Mikkel Beck's shot and the Dane followed up to score. Boro made certain of the points with Beck's second goal.
To cap Boro's day a water main burst after the match, forcing the ground to be evacuated in a hurry for safety reasons.
The Second Division leaders, Watford, were rescued by Tommy Mooney, who scored a last-gasp equaliser to earn them a point in a dramatic match at home to Plymouth Argyle. Mark Saunders seemed to have given Plymouth a surprise victory with only four minutes left.
With the point, Graham Taylor's side increased their lead at the top to three points as the only team close to them, Bristol City, lost 1-0 at Fulham. Paul Moody, who scored twice in a 4-1 victory at Plymouth on Boxing Day, was again on target as Fulham continued their improvement under Kevin Keegan and Ray Wilkins, moving into the play-off zone.
Northampton moved into third place, displacing Oldham - whose match was postponed - with a 3-2 home victory over Walsall, although they are still 13 points behind Bristol City. Recent signings Chris Freestone and Jason Dozzell both scored.
Notts County stretched their lead in the Third Division to seven points with a 2-0 win over Hartlepool with two Sean Farrell goals as their nearest rivals, Peterborough, lost 2-1 at home to Brighton.
Carl Griffiths scored a hat-trick as Leyton Orient equalled their record League victory with an 8-0 rout of the bottom side, Doncaster Rovers.Reuse content