Ok we have started trying to do this with a new course without deleting it from the production server. Same results so far. No user data.
Regarding the enrollment query: here is a partial screen cap of the enrollment page of the course on the production site:
Image may be NSFW.
Clik here to view.
as you can see the students appear to still be enrolled but still when restoring the course there are no students (or instructors) enrolled. (I'm not sure if this matters but we use External Database as the enrollment method for all of our courses.)
(to pre-empt any questions about the "Instructor" role: Yes it is a custom role. Yes it exists on both sites. Permissions are identical and both sites even share the same roleid.)
After verifying that there are no students enrolled in the course I manually enrolled the Instructor and all Students in the course, went into the Gradebook and all of the grades appeared. It is good that I can now see the data however we run hundreds of courses with thousands of students and we cannot possibly go through this process for each course.