by Stuart Mealor.
You ask: "What events causes a course to be flagged as modified for the purposes of the automated backups?"
Not an official response, but I have always assumed that ANY change in the course setup or content will be logged as a change, and therefore mean the course has been modified.
An obvious example is adding a new resource.
But from your question, I wonder if something like a synchronisation of users from an external system would also count - if the user data is updated in any way?
"We have 216 courses ..... system was backing up 25 courses and skipping the rest .... after upgrade to Moodle 3.4 it backed up 94 courses ..."
OK, so it's not backing up all courses.
So it's possible a setting that was at default before, has a new default now in Moodle 3.4.
As a first step, I would go through the automated course backup page, check, de-select and re-select the settings as you want them, and then see what happens.
PS - in terms of conserving server disk space, do you really need 40 copies ?