The striker suffered a hamstring injury early on in the 4-2 defeat by Notts County last weekend and faces up to three weeks on the sidelines.
Scott Wagstaff came on for Haynes and could have earned himself a start after scoring one of Charlton's goals and setting up the other.
Fellow winger Danny Green has returned to training after a shoulder injury kept him out against County and he could also be involved.
The Addicks are still nine points clear of Sheffield United in second.
Scunthorpe midfielder Michael O'Connor will return to contention following suspension.
O'Connor, sent off in the recent home win over Wycombe, has completed his three-game ban and provides manager Alan Knill with a welcome option.
Fellow midfielder Jimmy Ryan, recently recovered from the recurrence of a knee injury, is expected to be in the frame despite being replaced at half-time during the midweek draw at Yeovil.
Two more midfielders, Sam Togwell and Josh Walker, are pushing for recalls after being included on the bench following suspension on Tuesday night, but defender Christian Ribeiro, replaced at Huish Park by club skipper Cliff Byrne, remains doubtful with a hamstring injury.
Knill has no new injury or suspension worries as the Iron, six points above the relegation zone, look to extend their unbeaten run to five matches.