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So, bit of background first.

I have an Asus laptop with two partitions on the same disk, C: (OS) and D: (Data). I'd set all of my Windows default folders (documents, downloads, &c) to live on D: because it's much bigger.

Then I decide that I'm going to slowly move toward Linux while keeping Windows for the utility stuff I still need for work (like Civ5). I install Ubuntu on D:\ubuntu - bearing in mind there's still a lot of other D:* stuff, since I want to be able to access documents that I've stored there both in Windows and Ubuntu.

That install worked fine at first...I got everything installed that I needed to in order to be able to be using Ubuntu about 90% of the time I was using my machine. That lasted about five days. At one point, while I was using Windows, I got a notice that there were updates that needed installing; I let them install while I was shutting out of Windows.

When I restarted, I knew I should boot Windows first because it had to finish configuring updates. I got a notice that there may be some disk corruption on D:, and the menu wouldn't really let me go farther without running sandisk. That ran, I booted into Windows, let the updates finish, shut down again, tried to boot Ubuntu and got error messages which eventually led me to things like this: How do I remove the extra Ubuntu option on the Windows Boot Manager menu?

When I eventually booted Windows, I found everything (including the previously-mentioned Windows default folders) gone from D:. 100% free disk space, no backup, apart from the fact that most important files there were already Dropbox'd.

Now, I want to reinstall Ubuntu, and if possible, to have Windows go back to the practice of storing data on D: so I can access it while using either OS, but for safety's sake, I moved all those default folders back over to their normal locations on C:. I'm willing to give that up if that's what caused the problem (if anything, it might accelerate my departure from Windows), but most importantly, I don't want to go and do all of this just to have Windows wipe the slate clean again.

Any ideas?

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closed as off-topic by user68186, Alvar, don.joey, mikewhatever, Eric Carvalho Dec 28 '13 at 0:43

This question appears to be off-topic. The users who voted to close gave these specific reasons:

  • "This describes a problem that can't be reproduced that seemingly went away on its own or was only relevant to a very specific period of time. It's off-topic as it's unlikely to help future readers." – user68186, Alvar, Eric Carvalho
  • "This question is specific to an end of life Ubuntu release. These are no longer supported and are therefore off-topic here. To upgrade, see: How to install software or upgrade from old unsupported release?" – don.joey, mikewhatever
If this question can be reworded to fit the rules in the help center, please edit the question.

WUBI is no longer supported and it does not work on Windows 8 or later. In any case, WUBI was meant for short term use to try Ubuntu without partitioning the hard drive. You should consider full installation of Ubuntu in its own partitions. See – user68186 Dec 19 '13 at 2:41
So that would be a situation where I boot into Ubuntu by default and then start Windows from there if I need it? Incidentally, I'm fine with whatever not being compatible with Windows 8. Part of the reason I'm doing this now is to not have to switch to Windows 8 and if possible to do this without buying a mac. – Polisurgist Dec 19 '13 at 2:51
It is the installation that requires partitioning of the disk. Once Ubuntu is installed, you would get a choice to boot Windows or Ubuntu. If you don't choose anything it will wait and then boot Ubuntu by default (This default can be changed from within Ubuntu later if you wish). If you want to boot Windows, you have to reboot the computer and choose Windows when you see the choice before it goes to Ubuntu. You cannot start Windows from inside Ubuntu. You have to reboot and then choose just as you are used to in WUBI. – user68186 Dec 19 '13 at 3:26
I can do this (and am in the process, though the iso may take the rest of my life to download), though if anyone else has ideas on why the problem above actually happened, I'm still curious. – Polisurgist Dec 19 '13 at 21:36
I have no idea why the problem happened. Some limitations of WUBI have been documented.. There is also a troubleshooting section in the relevant Ubuntu Wiki. While these may not answer your question, they may help you understand the general problems with WUBI. Best of luck. – user68186 Dec 20 '13 at 4:37

Relevant part:

Corrupted NTFS filesystem

All reported cases of damaged filesystems were from users who hard rebooted (pulling the plug).

When you hard reboot, there is always a chance of damaging your filesystem, whether you use Wubi or not.

New users, unfamiliar with a new operating system, tend to hard reboot more often than necessary when they encounter problems.

If Wubi becomes damaged as a result of a hard reboot, there is a chance that Windows may also become corrupted since the principle behind Wubi is that of a virtual disk within the host operating system.

Sometimes people blame Wubi for these issues even though a quick Google search will reveal numerous cases of NTFS corruption without users having ever installed Wubi or ntfs-3g (and a full software industry lurking on that…).

If the NTFS filesystem becomes corrupted you need to run chkdsk /r from the Windows Recovery Console on the Windows CD (or other recovery CD available on the web) or in the msdos console (if you can boot into Windows).

At the moment there is no fsck for NTFS on the Linux side, otherwise it would be possible to fix these errors automatically within Linux itself, without having to rely on Windows tools.

The best advice is to simply avoid hard rebooting, whatever OS you may be using.

This means that even if you didn't used WUBI, your disk might fail if you perform the same action you did.

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