Pilot tone is generated by a crystal in the recorder and is very stable.  When transferring from the location sound tapes a resolver (generally built in to the Nagra)  is used to correct the playback speed of the location tape using the Pilot tone as reference.  Thus if the location recorder speed changed at all during the recording process, these fluctuations will be corrected.  A Nagra with Pilot tone will maintain perfect lip sync with an image recorded on a sync sound camera, provided that the camera is running at a stable 24 frames per second.  Pilot tone is recorded and played back  with its own special magnetic head which places the 60 Hz sine tone out of phase with the audio sharing the same 1/4" tape.