Deactivate: This option is best used when you want to remove a student from your Student Roster. If the student has work completed, they will not lose this work if/when reactivated.
Delete: This option is best used when a student has not logged in or completed work and needs to be permanently removed from the school. This can only be performed on student accounts that have not logged in. If a student has logged into the account at any point, it can only be deactivated and not deleted.
Please see the article for steps on how to Deactivate a Student.