Will the import handle the concept of the table having the user record in it more than once with different course numbers
Sure, no problem at all. This is normal behaviour, a student being enrolled in more than one course at the same time
Also how does moodle handle if the user does not yet exist? What if the course does not yet exist?
They are logged as non-existant users/courses, but are otherwise simply ignored.
there are basically 3 questions: Can the external database contain more than one record per student? What happens when a student does not exist in authentication but does exist in enrollment? What happens when a course does not exist in moodle that does exist in enrollment?
The answer to those 3 questions is: everything works as expected