Hi Navid,
The Reharmonist feature found in "Edit | Chords | Auto-generate Chord Reharmonization" is designed to work with a MIDI melody recorded on the Melody or Sololist track (if I'm reading the Help files correctly).
From your original post, you have recorded chords on the Melody track and not a melody. How these will be interpreted by the Reharmonist, I do not know. Try it and find out.
What I suggest you do before running any of these modifying routines is to save your song file as a MGU file first. Then save a second copy with a slightly different name and work on this second copy. Should you ever need to get back to the original file, it's then just a matter of loading in the first file you saved.
If you have recorded a chord progression, Charlie's approach will be a productive one.
My thoughts are that rather than using the Reharmonist, it might be more productive for you to use "Edit | Chords | Auto-generate Chord Substitutions".
If you've got a second copy of the original file saved, as suggested above (so you don't lose the original recording), I suggest trying all approached and seeing which one gives you the best results.
Regards,
Noel