Following steps in QA test http://tracker.moodle.org/browse/MDLQA-504.
[5. Access a course and follow the import link again.]
[6. Select 'Import deleting' and select a course to import data from.]
[7. Perform the import.]
On importing course data using the option 'Import deleting' all enrolled users on the course (you are importing into) are removed.
I would expect all users enrolled on the course to remain (especially as when this process is undertaken by a teacher if it's not a self-enroll course they have no way of then accessing it).