MongoDB 3.2.10 Index rebuilding did not complete: 11000 E11000 duplicate key error collection
I have deleted all data from dbpath and again restarted replica set sync and it looks it is going fine now. I was trying to restart a failed replica set sync and it looks like MongoDB was not able to handle it, once I cleaned up failed replica set data and restart mongo and looks like it is passed point where it was failing before.

Basically,I have removed host from relica set configuration, cleanup dbpath, restarted mongo and again added host in replica set configuration.