HI Luke.
I had this exact same problem when I wanted to update my scorm activity. What I had to do was create a stored procedure to automatically move all users to the last specific module that they had completed. For me it was relatively easy because my courses force users to achieve 100% (i.e., they cannot move past a question without getting it right) - if yours doesn't do this then it will be slightly more complex, but it's all acheivable, if you haven't yet deleted the tracking data (or have it backed up.
In order to do it, I went through the course myself and stopped at the start of each module then saved all the completion data (from mdl_scorm_scoes_track). Then I created a stored proc which allows you to specify the userid, the module id and the Scorm and scoid's. When you call it, it selects the tracking data for the user for that module, deletes the old and then re-inserts it. For me, I didn't need to specify anything in the mdl_grade_grades table as Moodle will do it for you next time it saves, but you may need to do that too.
I hope that helps. The short answer is, different modules (inc' updated) have different tracking data.
Hugh.