I think there might be a couple of "undocumented features" intertwined in this one...

To reproduce:

1. Log in as Admin
2. Create a new site-wide Standard scale
3. Add a grade item to Course1 using this new scale
4. Add a grade item to Course2 using this new scale
5. Make a backup of Course2
6. Go into Course1 > Grades > Scales
7. Edit the new Standard scale in Course1 by deselecting the option for "Standard scale" to make it just a Custom scale that exists within that course
8. The new scale moves from Standard scales to Custom scales
9. Go into Course2
   • Go to Grades > Scales (the new scale is no longer in Standard scales or Custom scales)
   • The actual grade item that used this scale still exists however, the Name of the scale listed in the field ‘Scale’ changes to: name-of-scale(Incorrect custom scale, please change.)" 
   • Go into Site Administration > Grades > Scales and notice that the new Scale has been removed here as well
   • This is both good and bad. Good for my purposes as I was looking for a quick and easy way to remove an incorrect Standard Scale for all courses (assuming this is why this functionality was put into place in the first place?)
10. Restore the backup from Step 5
11. Go into the restored course
12. Go to Grades > Scales and notice that the old Scale is restored as a Standard scale
13. Go into Site Administration > Grades > Scales and notice that the old Scale has been re-added as a site-level Standard scale for any teacher to be able to select from within their course

The behavior for the remaining courses that use a particular Standard scale (that has been “removed” from one course) is not what one would expect the behavior to be for all the other courses that may use that scale. Never mind that this old Standard scale has been re-created at the site level for anyone to use again.

Ideally wouldn’t you want the action from step 7 to just move the standard scale from that course without affecting others? Or have an option to remove from just this course or all courses?  I think the Standard scale should be physically deleted by an Admin, not “removed” when an admin chooses to remove it from one course.

Just my 2 cents – thank you in advance for any work that can be done on this as it’s a real nutty one IMO!!

This "undocumented feature" was also discovered (April 2023) in this tracker item https://tracker.moodle.org/browse/MDL-47461