Dan:

I recently had a similar situation (if I'm understanding your problem correctly).
With the harmony parts on the melody track, I ended up opening the Piano Roll
and selecting all the notes for ONE of the harmonies, and copying them to the Soloist track.
Then save the song WITH A NEW NAME.

Then you can delete the melody track altogether and print just the "Soloist" track
(which is now the first harmony).

Then go back to the original file and do the same for the 2nd harmony part.

It can be a pain selecting and then copying the harmony notes.
Hopefully, someone will chime in here with an easier way.
Let us know if I've misinterpreted your problem.

Good luck!
LLOYD S