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Of late I had been thinking of having a fresh install of Ubuntu. So I cut-pasted all my required files and folders in my E drive. Then I decided to not to have a fresh install and just let it be.

Later, when I booted up in Windows (dual-boot with 12.04 and Windows 7), I found that the files and folders I had cut-pasted from my home account in Ubuntu are just not there.
What is even more surprising is that now, when I am back on Ubuntu, those files and folders that should have been there in my E drive are also not there.

Is it an Ubuntu issue or a hard drive issue?

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Something like this is usually user error, something simple was missed. It is unlikely that your files were copied. Try again and make sure you are copying from one disk to a different disk (or partition). Wait for the transfer to finish. Make sure you are looking at the correct drive from both OS's. E: would be Windows, Ubuntu will see a label or SDA, SDB, something like that. Good luck and well done verifying the file transfer. Many people don't check and find out too late that the files are gone forever. –  Tom Brossman Aug 31 '12 at 8:56
    
@TomBrossman "E: would be Windows" ?? But surely Ubuntu allows me to access my hard drive media! And that's what I did. The files are no more there at original source location, and as I wrote they are neither there at the destination location. So, emm, are they gone forever!?!? And, I am very sure that the transfer was completed when I had done so. –  pnp Aug 31 '12 at 9:04
    
what's your "E drive"? how is it accessed in Windows or Ubuntu? –  steabert Aug 31 '12 at 9:25
    
@steabert While I am accessing the Home folder or any directory-> From the top menu- 'Go' -> Computer -> 250 GB hard disk: E. And in Windows, it is plain n simple isn't it- My computer -> E Drive. –  pnp Aug 31 '12 at 9:34
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Sorry, I should have made it clearer. 'E:' is something Windows would do to designate a specific drive or partition. Ubuntu uses a different way of identifying drives/partitions. If you were looking for 'E:' in Ubuntu you would never find it because it would have a different label, usually a name or drive label that is a word. –  Tom Brossman Aug 31 '12 at 11:26
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The problem is with hibernating Windows. If you start Windows it reads filetable of partition (your drive E:). Then when you let Windows hibernate, it has this filetable in memory and writes the memory to hiberfile. When you open Ubuntu, add files and then wake up Windows, it loads into memory the state before hibernate from hiberfile along with old filetable without these files. On Windows shutdown, filetable is rewritten by old one, so the files appear missing.

Do not write anything on that partition/drive and try some recovery software to get files back.

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So if I understand you correctly, you suggest against writing anything on those partitions when I am accessing Ubuntu and Windows was hibernated and not shut down. Is that right? –  pnp Aug 31 '12 at 9:05
    
Yes, NEVER write to shared partition, if it was not unmounted in windows and you let it hibernate. –  Jaroslav Bucko Aug 31 '12 at 9:08
    
What is a file table? are you referring to a partition table? in that case, I think, partition table is only gets written when you do things with partitioning. –  Anwar Shah Aug 31 '12 at 11:04
    
Master File Table –  Jaroslav Bucko Aug 31 '12 at 11:14
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I have tested this on 12.04. If you hibernate Windows, only the system drive is Locked i.e it cannot be mount as writable, but other partition such as E: is totally writable to Ubuntu. Also note, Locked partition can't be even mounted with nautilus (except doing some tricks such as mounting read-only or using remove hiberfile option), so this answer is not correct –  Anwar Shah Aug 31 '12 at 11:42
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