(While restoring M1.9 course archives into M2.2)
In our experience, the restore is behaving as it should.
It's our theory that when using the Merge option the section headings of the destination course (the course being merged into) are being protected against being accidentally over-written by the section headings from the backup archive. (I looked, but couldn't find any documentation supporting this theory.)
During the restore process, in Step 4 Schema, there is an option for "Keep current roles and assignments". This maintains the destination course's enrolments (and enrolment methods?) for us. We're using LDAP, if that's important.
We recommend our faculty use "Delete the contents of this course and then restore" to restore their courses. But then again, they are typically restoring into a blank Moodle course shell in any case.
Hrynkiw
Kwantlen Polytechnic University