Are there any other used tracks below the source track? RB is pretty adamant about not writing to a track that it thinks already has data. Also to tracks that are designated as BIAB tracks.

Sometimes even if you've deleted data from a track, RB still remembers it used to have data, and won't let you do certain things to it.

You may just need to move your source track to the very bottom of the project before trying to apply harmonies to it. That way all tracks below it will be clean and available.