Time Machine backup set is missing some files

Question

Today I noticed that some files I last worked on in August have disappeared from my computer. They were pdfs, word and vectorworks (cad) files in different folders – they could not have been accidently trashed. They were active work files from May until late August so they should have been backed up by Time Machine sometime in the past few months. But when I browse the backup sets these files are nowhere to be seen (and of course my daily Superduper bootable clone doesn't have the files either).
The external usb hard drive for Time Machine and the computer are clean according to disk utility, and I've run Onyx a few times to fix permissions.
Does anyone know why files would disappear from both the computer hard drive and the backup sets?

Answer 1

peterkhill wrote:
Thanks for your response. I know it's a mystery.
The files - in some version or other – should be in one of the backup sets, but they aren't. Time Machine hasn't started to delete old backups, as there's plenty of space on the external drive.
Not true. Time Machine "thins" backups normally, regardless of space.
As noted on the TM Preferences panel, it keeps one backup per week for as long as there's room; one per day (the first) for a month; all others for 24 hours. Every time it does a backup, it does "post backup thinning," deleting "expired" backups. So, depending on how long something was on your internal HD before being deleted, and just when various backups were performed, copies of deleted items can disappear as early as 24 hours, or as late as your oldest backup.
I've checked the backups with Timechecker
Do you mean TimeTracker? If not, and it's useful, do you have a link?
and it seems these missing files were never backed up, even when similar files in other folders nearby have been backed up properly.
The Do not back up box is as it should be in Timemachine - the files should have been backed up.
But then the files should still be on the internal HD too.
All I can think of is that the files themselves must have been corrupted somehow, but they are different file types, completed on different days, before and after files that appear to be OK on the internal and on the TM backup. And they must have been corrupted in a way that means that they cannot be found on either the internal HD or in the backup sets.
This is not something I've seen before (and I read at least the title of every thread here). The only thing I can think of is some sort of directory corruption that caused the originals to disappear, and the backups then, eventually, were deleted in the normal fashion.
By the way, I'm not running FileVault.
Do you know of any good data recovery applications?
The one I see here the most is +Data Rescue II.+ I can't recommend for or against it, not having used any of them. They are expensive, and there's no guarantee, although some have a free trial mode that will tell you if anything is recoverable, and perhaps let you recover one file.
Check Google, VersionTracker.com, or MacUpdate.com for +Data Recovery.+ Make certain whatever you get is compatible with Leopard.
Let us know if you have any success.