I'm not sure if this is the same issue but when I got my current pc with an ssd and hdd I followed a guys advice to changed some file paths in regedit, things like programfilesdir etc to have more room on the ssd. Apparently this could be done on previous versions of windows, and maybe some win10 versions. But on mine it nearly ruined the pc. I had only changed 2 paths in reg edit. I noticed some apps no longer worked, as in win10 couldnt even see them. Win10 couldnt see the app store. Also windows updates kept failing too. Oh and my usb connectors didnt function correctly either.
The problem 'appeared' to me only when I updated to the 1151 windows. Prior to that it worked before the update. So I ended up rolling back to the previous version.
Because at some point I did want to update windows I ended up changing the regedit files back and using the media creation tool to overinstall the new 1151 version on to the computer. All paths got restored and everything is working again.
I found out after you can actually set the drive paths by going to Settings->Storage and setting all those save locations to the drive you want. I have all new apps, documents, music, photos and files and tv programmes will be saved to my drive D. So that did the same job I was trying to do with the regedit.
I noticed the guy on that site was using bitlocker to encrypt his hard drive. I'm thinking that is his main problem. I remember using a file encrypter some years ago... bcwipe i think it was called. It had an encryption part and that give me blue screens.. I noticed they only started happening when I had that on the computer, even though I wasnt actually using it at the time it still caused me problems. So I uninstalled it.
If your not using an encrypter and you havent changed directory locations in reg edit you should be ok. If you are still concenred that make sure you take a backup image before you start.
I've not used this myself but I hear good reviews of the program. Its cloning software. Macrium Reflect Free Download - http://www.macrium.com/reflectfree.aspx