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My brother told me two weeks ago that some of his files were missing and last week all of his files disappeared (together with some installed programs). The weird thing is that the folder structures are still there - it is just the files in the folders that are missing.

It seems that I can recover the non-backed-up files with photoRec (of testDisk), but would like to know what can cause this and how do I prevent it from happening in the future?

P.S We did clean the computer with an air blower right before all the files disappeared, but I doubt that this can cause it seeing that some disappeared before then and the computer only has xUbuntu 13.04 on it.

EDIT I forgot to mention that all configs were also reset (launcher(s) settings and background, including email accounts).

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    Any cloud syncing software running? Other people who may have access? What applications usually open these files? Syncing with external USB devices? Just to list some of billions of possible causes to look out for.
    – Takkat
    Jun 24, 2013 at 8:54
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    @Takkat ownCloud is running, but only on the documents folder while all the files in the home directory have disappeared - so can't be that (hopefully). Also see edit that will rule out the other and why I'm a bit worried about it.
    – chesedo
    Jun 24, 2013 at 9:05
  • Is there another account on that machine also affected? Are the HOME directories on a separate partition? Any applications crashed before this happened? Were there another user account or any other directories outside /home/<yourbrother> created?
    – Takkat
    Jun 24, 2013 at 9:21
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    Check your system logs (e.g. /var/log/syslog + archives) for filesystem check automatic "fixes". If you have silent data corruption on your disk drive, this can cause inodes to be deleted or much worse things can happen. Also check the SMART state of your hard drive in "Disks" (maybe you need to install gnome-disk-utility on your system first). I have seen the very same issue with an OCZ Vertex SSD - it was almost dead and just before it corrupted my data badly.
    – gertvdijk
    Jun 24, 2013 at 9:27
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    I would not be so sure the air blower had nothing to do with data loss. For example, if you got dust in the hard drive rather than out of it, this could explain data loss.
    – don.joey
    Jun 24, 2013 at 9:49

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While this 'could' be a failing disk, the fact that no other directories were affected makes me think that it's more likely something else. Once (or twice), I've accidentally deleted EVERYTHING on my drive and it acted exactly the way you are describing this. Most of the files were gone instantly but a good portion didn't go away until all processes which used them also quit. In summary, my guess is that your brother ran something like: cd ~ && rm *

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