We're experiencing the same issue. And it would be awesome if we didn't need the completion data, but we're consolidating instances, and this data is basically what we need from the course. Backing up user data in general from Moodle and trying to restore it just seems to be generally unreliable and bad when going between different versions or sites. Actually, loads of different "Duplicate key value violates constraint ****************" errors for various different tables. It's super frustrating. So frustrating that I'd rather just have the raw SQL queries that the restore is doing so I can run them myself. I'm spending that much time in the database anyway fixing this stuff.
At any rate, if I find anything, I'll post it back here. I've only spent two weeks on this, so I'm basically just getting started.
by Peter Carpenter.