I have noticed a problem with Time Machine on OS X Mavericks: it drops files from the backup, and once they are dropped they are never backed up again. You can see the extent of the problem by running a backup, forcing a full file system travesal, then backing up again. It will backup gigabytes of previously missed files.
One folder where it is easy to reproduce the problem is the user's Preferences folder. I just ran an experiment: I forced full traversal, so it backed up all 353 items, then checked it after each backup. It was fine for 7 backups, but then dropped from 353 to 145 items. It clearly backed up every item until a certain point and then skpped the rest of the folder. (Actually, it stopped making hardlinks to the unchnaged files.)
A difference in the problem Time Machine run was that Sophos Anti-Virus for Mac (9.0.11) was performing an update simultaneous with the Time Machine run. We know from the problems with Sophos 8 & Mountain Lion that the Sophos auto-update tends to run at the same time as Time Machine, because both kick off soon after waking the computer up from sleep. The previous problem was that the Apple installer used by the update would change Time Machine to exclude large parts of the file system, causing a bad Time Machine run.
This is a different problem. For one thing, the folders affected aren't once that are excluded by the installer bug. Another is that doesn't recover from the problem in the next backup. And Time Machine is backing up (creating hardlinks) to part of the folder before abandoning the rest.
My question is: Is there a contention or compatibility issue where the Sophos signature update can interfere with Time Machine? Such as, the reloading of the live protection kexts interrupting Time Machine's file system access?
If so, whose problem is it? Sophos or Apple?
Attached are the logs for the Time Machine run.
Note: This is a bigger problem than just this one run. What I see is over time more and more files are missed in the backup, and then never backed up again. If there is a problem with Sophos & Time Machine, it would explain it, due to the timing characteristics of the Time Machine backup and Sophos auto-updates.
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