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I had created an NTFS partition (using the default Windows File Manager) (~500 GB) as the common partition between my Fedora 17 and Windows 7. It seemed to be working fine until I realized that the folders (and their contents) created and modified in Fedora weren't showing up when I was using windows to access the same drive. Now my Fedora has become corrupt and I have no way of finding out whether my data is still there or not.

Please help me in understanding what happened and how shall I prevent it from happening it again

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Were you using hibernation in Windows? – Karan Jan 5 '13 at 20:20
I guess I was... Is that the reason? – vedant1811 Jan 7 '13 at 8:06
It could very well be. Should be easy enough to confirm. Disable hibernation in Windows, shut down, power on, boot into Fedora, make changes, reboot into Windows and confirm that the changes persist. – Karan Jan 7 '13 at 20:55
I will do that. Now I have windows 8 and there is no hibernation. I will have to recover ferdora first since presently it refuses to start. Thanks for your help – vedant1811 Jan 9 '13 at 8:19
@vedant1811 Windows 8 still can hibernate (try shutdown /h) and it's default hybrid shutdown uses hibernation too, so the problem will persist. You should disable hybrid shutdown or shutdown Windows using shutdown /s /t 0. – gronostaj Mar 9 '13 at 10:23

The reason is closing windows in hibernation (win 7 and win 8) or restarting (win 8 only because it uses "fast restart"). This prob is more or less solved in the newer versions of the Linux distros ( like fedora 18 and ubuntu 12 ) since it warns that the "hiberfile" exits and should be deleted or the drive should be mounted in read-only mode.

Data loss was because I ran the pre windows load tool that "checks and fixes for HDD consistency". It removed the indices that were created by Linux leading to whole folders (that were created in Linux) vanishing.

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