Neymar will play as a wide player in their set up. As far as I know, Fabregas never played in the wide role - it was always Pedro or Tello or Iniesta or Sanchez or Villa who occupied the place that will be taken up by Neymar. As a result, there is the possibility of Iniesta playing more in the midfield which will affect Fabregas' game-time, for sure. In Messi's absence he played the "false number nine" role, but, clearly failed in big games. Now, he'll go down on the pecking order for that role after Neymar's arrival.
But, the position they'll looking to play him at is the most advanced of the three central midfielders which happens to be his stock position. He is obviously not a like-for-like replacement of Xavi, but, plays in the same larger position. It would be stupidity for them to let go of him at this point of time after Thiago has been shipped out.