To replicate the issue:
1) make a backup
2) In a GURU front-end, let the super administrator (SA) finish a course and the final exam.
3) make a backup
4) Then, in GURU backend, reset the SA scores.
5) logout then log in as SA
If the same happens to you, then the SA looses his SA status.
If he's not also in another back-end group, like 'administrator', he may also no longer be able to log in to back-end.
Before and after I reset the SA scores I made an Akeeba backup.
When I tried to restore the backup I made AFTER, I was no longer listed as Super Admin in the restoration process.
Only by restoring the backup made BEFORE I reset SA scores, could I again see me listed in as SA.
For security reasons, I can't add strangers to this website's backend.