Hi @FlemmingVesterg 

All SIS Import integrations are based on using the SIS ID as the unique identifier.  If the courses "got new SIS-ID's", then they are essentially new courses, as far as Canvas is concerned.

If you are trying to track down missing courses and course materials, my first step would be to go to Settings > Reports and run a "Provisioning" report, selecting "All terms", "Courses", and "Include Deleted Objects", to see if the courses you're looking for have been marked as "deleted" by your SIS integration process due to the changed SIS IDs.