Thanks for the response Dan - what I am finding is that if I edit the Scorm settings and specify a new object, the original scores are getting removed.
Is there a specific set of steps I need to do to ensure this is not the case?
I am also testing external repositories to try to get this working, but would far rather be able to just upload a new object directly into the course. Would it be a useful thing if there was a checkbox alongside the Scorm object uploader that allowed you to say this is an updated version of the existing object, and this in turn would force Moodle to retain the scores from the original object and apply them to the updated one?