I remember on older versions of PT that the muted regions would unmute and become part of the consolidated selection, but that was a long time ago. The muted regions should be replaced by silence.
Just a simple tip. Before you consolidate, make sure you do a playlist of the track. This way if you ever change your mind about something you muted, you can always retrieve that part by referring to the saved playlist.
Dave Reitzas
htpp://www.reitzas.com