The 28-year-old midfielder underwent a medical and agreed personal terms with Bayern Munich before the move fell through on deadline day.
Fulham could not secure a replacement for the Portuguese and the German champions ran out of time to sign the player.
Palhinha is back at Fulham but Bayern Munich are still claimed to be interested in getting their hands on him in the winter window.
It has been claimed that Silva and the Fulham hierarchy are not on the same page regarding the player’s future.
The Fulham boss does not want to lose the midfielder and wants to fight to keep him at the club.
However, the club are open to letting Palhinha leave in January if they can secure a proper replacement in the middle of the season.
His agent recently indicated that Palhinha’s departure from Fulham has only been postponed and not cancelled.
