If you come up with a soup that is able to generate useful melodies, rhythms, chords, velocities etc. you can take a snapshot of the soup with print-soup.
(initdef)
(defsym a '(a b c))
(defsym b '(b a c))
(defsym c '(c))
(init-soup 'soup (gen-trans a 3))
(print-soup 'soup)
-->
(def-soup 'soup
'((d e d) (c d e) (e f d e) (f e f) (a b c d) (f e f d e f))
'((d f c) (e d f) (f c d) (d e) (d e f e)))
When you copy the output in the source file and evaluate it before gen-catalyze you'll be able to restore a soup.