
Clarke joined the National League strugglers - one of his former clubs - on loan until January just before the Carlisle game.
He made his debut in Oldham's 2-0 defeat at home to Barnet - a result which dropped them into the National League drop zone.
Flynn said there were reasons behind Clarke going back up North outside of on-field matters but they would remain in-house. He said: "There have been no fall outs or anything like that, but there are good reasons for him going to Oldham.
"He is a fantastic guy and a great professional and it will do him good to get some game time there at a club he knows well."
Clarke played with Flynn at Blackpool and has had a previous spell at Oldham between 2016-19 when the Latics were in the football league.
The 40-year-old is a veteran of nearly 900 league games in a 23-year-league career.