The Northern Ireland international refused to board the team bus heading for Wycombe on Saturday less than 24 hours before kick-off.
It is understood contracted players, including Magennis, were paid their overdue wages on Friday lunchtime but that there was a discrepancy which threatened at one stage to trigger another player strike.
Five senior players did travel to Wycombe – Remi Matthews, Jason Lowe, Erhun Oztumer and Luke Murphy anchoring a side that also included three signings sanctioned on the morning of the game: Harry Brockbank, Josh Earl and James Weir.
Parkinson admitted his frustration, however, that Magennis had dropped the bombshell so close to the team travelling.
“Josh put in his notice like quite a few of the lads and he was obviously hugely frustrated by not being paid for five months,” he told The Bolton News. “He put that in, the administrators appealed against it, and there is a hearing, going forward.
“My gripe with Josh is that he told us just as we were walking out to training and we’d picked the team and he knew we were already struggling.
“We know he is a very emotional lad, and it has affected him mentally in terms of what has happened, his career, and not getting any money.
“We will have to wait for the hearing to see whether Josh stays or whether he goes.”
It is not yet known when Magennis’ case will be heard but Parkinson says he will speak with the 28-year-old this week to assess whether he could be involved in next weekend’s home game against Coventry City.
“It was quite a brief chat I had with Josh, a rather heated exchange as you’d imagine,” the manager said. “We were already under immense stress as a management team coming into this game.
“But when the dust has settled over the weekend we’ll assess what damage has been done.”