10.5.8 - Horrible update problems, Time Machine failures

Question

I've just had the singular worst experience involving a Mac that I've ever had. I don't think anyone can actually fix what is wrong with my computer anymore, but I feel the need to describe my experience. Perhaps someone out there can tell me what went wrong, where, so at the very least this isn't repeated.
I came into work this morning, unlocked the screen of my Mac Pro, and the software update bouncing icon was letting me know that I still hadn't installed the 10.5.8 update. I figured, okay, fine, while I make some coffee let's do the update. Software Update does its thing, restarts my computer, and, boom, I'm back at a login screen.
I log in to the computer, and I have the default Leopard background. Not only that, but I notice that my dock icons are the default Leopard icons. Now I'm nervous, so I check out the finder. Yep, nothing in my home directory. I do, however, see a sparse bundle. I double-click on the sparse bundle, enter my user password, and voila; there is everything that should have been in my home directory.
I figure this has to be some kind of reasonably simple problem with recognizing a File Vault home directory. I then proceed to do what many Mac users have to do with every single OS update; go download the combo update and pray. After downloading the 800 MB combo update, I install it, reboot, and find that I still have the same problem. On advice that I found on the Internet, I try rebooting in Safe Mode, reinstalling the combo update, and logging in again. Still no dice.
This is where things get really fun. I think to myself; this is horrible, but I have Time Machine! I can just restore the machine to before I installed the update. After poking around, I find my Leopard install disc, order the machine to reboot with the disc as a startup volume, and away I go. Here's where I made my first mistake (that I'm aware of!). I went to the system restore utility, and it informed me that it would wipe the hard drive.
At this point, alarm bells should have been going off. After all, it was clear that nothing was working the way it should. Unfortunately, I had utter faith in Time Machine; I mean, what's the point of a backup utility that you can't trust, right? So I say, hey, sure, go blow away my hard drive. At this point, I go to have lunch while it does its magic (because, yes, trying unsuccessfully to fix the problem took my entire morning away from me).
When I come back, I'm thinking to myself, "maybe I should have backed that sparse bundle up to a spare drive just in case . . .". Sure enough, I restart, and just like before, I have an empty home folder. The only difference is that, this time, there is no sparse bundle. There is no record on Time Machine of any backups of my home directory. Not only that, but even though I restored to one hour before the 10.5.8 update, the files on my machine are no longer the correct versions.
I work on my development files out a subdirectory of /opt (don't ask). I go in to the subdirectory, check the Git repository, and find out that I'm 7 commits behind the master. This is odd, I figure, since I restored to one hour before the update and I haven't even touched the computer since Friday.
So, here are the problems I faced:
1) The 10.5.8 update completely ruined my system's ability to access my Filevault protected home directory
2) The 10.5.8 update apparently does not allow Time Machine to make a current backup of the user's home directory (as is normally done as part of the shutdown procedure - this is the only explanation I have for why Time Machine did not have a record of my home directory)
3) Time Machine did not restore the correct version of my hard drive's files
4) Time Machine did not keep a record of my home directory, AT ALL
So far now I've lost roughly three quarters of a day of work, and I will lose at least another day or two as I try to track down what versions of my files Time Machine actually restored, try to incorporate any necessary changes to those files that were passed over by the system restore, try to find a backup of my home directory that is not from Time Machine (which will, because these backups are more irregular, mean that I'll still have at least week old files and thereby lose a full week of work for anything not committed to a repository - at least I can be thankful that I do have other home directory backups, and that I don't rely on Time Machine for everything - if I did, I'd be completely hosed), and then proceed to get my machine back to a reconfigured, workable state.
The question that presents itself is when, if ever, should I contemplate doing the 10.5.8 update again. I will now forever be terrified of Apple OS updates; I can't believe the amount of work that has already been lost to this nightmare, and the amount of work I am going to have to do in the coming days to clean up this mess. If I could have pinpointed what would be the worst possible update scenario I could think of, this would be pretty close.
I hope no one else has faced any similar problems in their recent updates, but if they have I would certainly like to hear from them regarding what they did to alleviate the issues.
Thanks for reading and in advance for any help, advice, or considerations for the future you can provide.

Answer 1

baltwo wrote:
A Time Machine backup is only as good as what can be restored ...
This much is true of any backup.
... since the backup isn't checkable until you restore it
Fully checking a clone (IOW, not just that it will function as a startup disk but also that all the files it contains are readable or usable) is extremely time consuming. And since it is a duplicate of the volume it is backing up, it can & usually will inherit any problems of that source, especially if the copy method is a block (as opposed to file) copy. For this reason, I use SuperDuper! to make my clones, since unlike CCC or Disk Utility it always does a safer if slower file copy.
However, there is still the problem that the clone will not automatically contain a file or container (folder or package) inadvertently erased or replaced with another one of the same name on the source, or a good copy of one that has been damaged on the source since it was installed or created. IOW, a clone is a snapshot of the source volume state +at only one moment in time+ -- including any problems or omissions of that source at that moment in time.
Archival backups like those made by Time Machine or Retrospect are different: as these product names suggest, they can back up the state of the source volume at many different moments in time to one backup volume. Moreover, particularly with Time Machine, they make it quick & easy to locate a particular version of some backed up item & restore it if needed. With Time Machine at least, one has the option of replacing an item or keeping both versions, with one renamed with an "(original)" suffix, since this kind of restore is basically a Finder copy. Occasionally "entering" Time Machine's galaxy timeline interface should make it obvious if things are being backed up or not. For instance, if there is no home folder in /Users/ for some user account, it is obvious that account isn't being backed up.
Unfortunately, everything changes for FileVault encrypted home folders. You may not even see the encrypted home folder in a Finder view of the Time Machine backup. When you turn on FileVault for an account, you get a warning about its consequences for Time Machine backups:
+Time Machine backs up home folders protected by FileVault only when logged out. You cannot browse items of the protected home folder in the Time Machine backup. Because you cannot browse the items in the Time Machine backup, you cannot restore individual items.+
IMO this makes Time Machine a poor choice for archival backups of FileVault home folders.