I've been looking through a lot of this same issue here and elsewhere, and I'm appalled at the misdirection and finger-pointing that some people are throwing out. It is useful to run a Disk Repair, but when a file is missing, it's missing and you can't bring it back with a Disk Repair. Doing a Disk Repair might tell you that something was wrong with the directory structure that could have been involved in causing the files to disappear - but it doesn't help explain why files disappear when Disk Repair doesn't find anything wrong with the directory structure. And I've gone the extra step and used DiskWarrior to further test the drive.
I'm running Lion on my iMac. Everything is always kept up to date. I recently discovered many missing files in my external drive. Here's the scenario: Folder A contains folders B, C, and D. There are files in all of A, B, C, and D. Suddenly, all files in B, C, and D disappeared. A Disk Repair found nothing wrong with the drive.
I have been involved with some of my clients who were running Snow Leopard. One of them lost dozens of photos from iPhoto, the other lost several different kinds of files from different places. I carefully examined their systems and could find nothing wrong, and my job is to know how to find a problem with a Mac and fix it. I have also ruled out anything that might have been user error.
So, as far as I'm concerned, this condition of disappearing files has been around for a while. If Apple doesn't want to acknowledge it, it's only because they haven't experienced it themselves - and nothing that happens in the field can ever be verified or reproduced on command.
The one and only way I know of that would help track this down is a full Time Machine backup of the drives involved. In my case, I would need a 5TB drive. And since files disappear from external drives as well as internal drives, it would also be necessary to have multiple Time Machine drives to swap in and out periodically in case the OS decides to wipe out files in Time Machine. Then, rather than wait to discover that a file is missing, the content (structure) of the latest Time Machine backup would have to be compared to previous backups and a report provided showing the differences. This can be done fairly easily using a shell script - something I am quite experienced doing - and it might even be turned into a utility app. Something for me to work on. But even with this, it might take months before the user notices that the report is showing missing files that should not be missing. Human interaction is required for such a report. And on a daily basis, the user will delete files, so taking notice of which ones that are really missing will require some intense scrutiny and awareness by the user.
That said, Apple needs to step up its own analysis of disappearing files - and quickly. And this means acknowledging that such a thing actually happens.