All of your companydata should have www-data:www-data for owner/group - recursively. Safe to do as that directory is NOT directly accessible via web browser.
The 0 byte log files in temp/backup/ are normal an indicate a successful backup process completed. The long named directory with partial contents of a backup is the course that failed. Cron job/task should clean that up, but in this case ok to manually remove everything in temp/backup/
Wow!
462802906 Feb 14 06:13 questions.xml
question bank for that course is 462 Megs ... that's a lot! Am guessing that is the culprit in copy course.
xml files are asciii and you could cat 'em with |more to see structure.
For that course, one might need to do the old backup - from command line - maybe even with a nohup in front - to admin/cli/ and then a command line restore to a category. Moosh has a command for that.
You are close!
'SoS', Ken