Baudry was expected to return to training by the end of August as he recovers from Achilles surgery.
But he has this week visited his surgeon with the healing process taking longer than first hoped.
"Baudry has gone back to the surgeon and he's probably going to be one or two weeks more than we thought which is a bit of a blow for him," Ferguson said.
"It is healing but it's taking a bit longer than we thought.
"I would be guessing that Baudry and Luke McCulllough would be back around a similar time, around the end of September.
"Jordan Houghton will be joining us at a similar time so you're thinking about those three will be coming back not far off each other which is a massive bonus because we've got six or seven games in September."
Ferguson also revealed that Ross Etheridge is making good progress in his recovery from a broken ankle.
The goalkeeper had been transfer-listed by the Rovers boss at the start of the summer but his injury ensured he would remain at the club beyond the end of the current window.
Ferguson had spoken of potentially coming to an agreement with the 22-year-old to release him in order to join another club once fit.
But he insists the priority is to get Etheridge back to full fitness before deciding on his future.
"We've got to make sure we get Ross back," he said.
"He's back off the brace and doing a little bit more.
"He's doing well and he's working hard.
"The thing is, even if the window shuts, we can still loan him to a non-league club.
"We've just got to make sure he's ok in terms of his fitness."