I have been using Moodle since 1.9, and this backup problem really came into its own when they started content-hashing filenames. I don't agree with the decision to do that, but it is the way it is...
That said, Ken seems to be the only one who is tackling this issue. It's a common one, and one I have experienced with ever Moodle version. It seem simpossible to get Moodle HQ to think that its a prolem that needs solving, because maybe it isn't happening with many users, or maybe many users aren't paying close attention to their backup routines. In any case, I DO know that several people, including myself, are tired of having to hold our tongues just right to be able to depend on our backups. After all, if yo uhave a bad backup, and don't know it until its too late, then you are playing with fire. Personally, I like to not only have good backups, but have the ability to test the integrity of said backups. Lots of people THINK their backups are valid, and only find out when its too late. I just talked to a good friend who works in a big company who preaches "BACKUP" to his co-workers. But he sheepishly admitted that HIS hard disk went down on a critical mission, and he spent hi sentire vacation rebuilding the data that had been lost because......HE neglected his backups!
We tend to get complacent about this issue, and I think that moodle HQ owes it to us to make this backup routine bulletproof - both the manual one and the automated one. We shouldn't have to worry about these issues, and I would dare say that it has even caused some people to lose or endanger their jobs because they THOUGHT they had good backups. Plus, it gives moodle a bad name in the academic community.
Where I work, there is a fight going on between moodle and other non-free LMS systems for control of the academic market. I am a moodle evangelist, and do not want to see these other systems. But in good conscience, I cannot look the IT guy in the eye and say "Moodle is secure", because it is not.
Nowadays, enterprise systems DEMAND (rightly so) secured data about students, secure logins (using, for example SSL), and secure backups of not just system data, but historical data.
I would like to see the ability to archive users in such a way that I could clear a course out of all users and archive them in one step. Then, that data file could be stored somewhere securely and restored by data record. For example, if Danny Boy claimed that he got an A in Ms Meanie's course in polliwog research in 2008, then all we would have to do is go to our 2008 archives, find Ms. Meanie's class, and find Danny Boy's record. If the course wa sno longer taught, then we could find the transcript of Danny Boy, and perhaps see all the tests and assignments he took.
As it is today (as I understand it), we would have to restore an entire course including all students, then find Danny Boy and drill down to find just his information. That's such a bad way of doing things in today's modern computing environments.
But, back to the original issue. Wouldn't it be great if someone who is way smarter than me, could write a script that runs in the background and extracted the relevant .mbz file and copied it to a directory of our choice? Likewise, wouldn't it be great if there was a script that automagically fixed automated backups that stalled, instead of just having a report that says "Incomplete" Error handling is CRITICAL to a smooth running app. Moodle, of course, is user-supported app. But if it were being sold by a for-profit company, this backup problem, if not fixed, would cause the software company that produced it to go bankrupt. It really is that important. I only wish I could get moodle HQ to agree and to help fix it.