when auto-update is set it will check the scorm zip and rebuild the data in Moodle - this unfortunately changes the ids of the scos in the table. In Moodle 2 we disable that setting in places when it doesn't make sense so we prevent this from happening a lot more.

The main problem is that Moodle relies on the order of the scos listed in the database table - so if an updated SCORM package contains new scos or removes scos it needs to re-create the entries in the table - the code doesn't check to see if this is needed, it just does it every time an update is require deleting the old scos and recreating them again with new ids.

I would like to rewrite the code at some point so that we don't need to do this anymore and any new scos can just be inserted and the order updated but this isn't a small bit of work and no-one has offered to fund my time to improve it.

little bit more info on this here: MDL-34746