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.