The Mystery of the Missing Files: Windows 8 versus NTFS
I've been having problems with my computer recently. A few files would not be where I remembered them, or they would be missing entirely. Little problems that could have been my memory playing tricks on me. Then the little problems became a big problem when a collection of work files disappeared. Initially I suspected the hard drive; there were some bad sectors reported on the disk with the problems. Then it happened on other drives. 3 physical disks were affected by this, so it was not likely to be a hardware fault.
I dual boot Ubuntu and Windows 8. Windows gets used infrequently for gaming; day to day use is in Ubuntu. My files are on NTFS formatted disks, separate to the OS partitions. I finally spotted the correlation between OS and missing files after the virtual hard drive for a VM I had set up vanished - directly following a reboot into Windows. The little missing files suddenly fell into a pattern of my Windows activity.
Eventually, I was able to track down the problem. Windows 8 has a new feature called Fast Startup. It merges power off with hibernate, to reduce cold boot times, and is enabled by default. Fast Startup saves the state of all mounted drives on shutdown, including which files are present. After rebooting into Linux, I alter some files, and create others. I then reboot into Windows. The drives are compared to their saved state, and the differences are "repaired" back to how Windows remembers the drive being. Result: all the files added in Linux are removed.
Chkdsk was able to recover most of the files. Fortunately, Fast Startup can be disabled in Windows' power options (Control Panel>Hardware and Sound>Power Options>Choose what the power buttons do). All seems to be working now so hopefully this will not happen again, and I can stop worrying that I'm losing my mind.
Moral of the story: If you dual boot with Windows 8 and have shared partitions, you may need to disable Fast Startup