This is a bug and improvement issue in one:

Currently, if the "del" command is used, flatfile only unenrolls the user if he/she was enrolled through flatfile. If the user was not enrolled through flatfile, the admin email notification/log states that the unenrollment was successful, even though it was not. The user is still enrolled in the course.

Flatfile should allow that the "del" command (to unenroll users) is applied no matter if the user was enrolled through a flatfile, self-enrollment or other method.