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I have a dual boot system consisting of Arch Linux and Windows 7, with a shared partition to access files from both systems. Until a couple of weeks ago, I was predominantly using the Windows OS as I needed Windows only programs daily for my work. Now however, I do not require those programs and so have switched to using Linux virtually all the time.

I have used Windows twice in the last two days, and each time I booted into Windows, it ran the chdsk utility and subsequently deleted a whole lot of files from the shared partition. I didn't notice it the first time, and then found a whole lot of files were missing, but I just booted into Windows this morning and it happened again. This time I watched the output and it showed a whole lot of files being deleted. There were some new ones that I had only just created in Linux, but also older ones that I had made in Windows.

This wasn't a problem (it didn't happen) when I was predominantly using Windows. I could use Linux for a bit, then restart in Windows and it would be fine. Now that I am using Linux more though, this has started happening.

When it happened the first time I wondered if I might have a virus and so downloaded Avast for Linux and scanned the partitions accessed by Windows but that didn't find anything.

Any ideas on what might be causing it?

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Have you tested the disk for problems? Perhaps use the utilities offered by the HDD manufacturer? –  Ƭᴇcʜιᴇ007 Nov 11 '11 at 0:45
    
@techie007 I have done a check with the utility provided by WD and it founds no errors with the hard drive. –  anpro Nov 11 '11 at 3:59

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