Barton has expressed his desire to rejoin Marseille after a successful spell on loan at Stade Velodrome last season.
Marseille are thought to be keen on signing Barton on a permanent basis if he can free himself up from QPR by cancelling his contract at Loftus Road.
Baup admits Marseille and Barton have agreed a deal, but says everything depends on QPR with the 30-year-old still having two years to run on his contract in London.
"Joey Barton's comeback? I do not know how it will evolve," Baup told L'Equipe.
"The club and the player agreed about the challenge ahead, but he still belongs to QPR."