Started having some problems with my Windows 8.1 laptop. Troubleshooting lead to problems with some system files. System File Checker couldn't fix the problems, so I did the Windows 8.1 equivalent of the older Windows Repair, which is now called Refresh.
Things started out well enough, the Refresh program warned me that programs installed from the web would be un-installed, my Windows Store apps would all be reinstalled, and all of my settings would be kept.
Now, I KNOW, I should have backed everything up first, but I didn't. And well, that's not exactly what happened. Numerous programs were uninstalled, including Microsoft Office 2010. That one came as a bit of a surprise. Of all the programs installed on my laptop, I thought for sure that that one would remain, but it didn't.
In addition, quite a few of my settings were reset. Things like my Outlook profile, were now gone. I was back to those annoying check boxes for selecting icons (who came up with that?). Preferences for using my fingerprint scanner to login, my HotMail/Outlook.com account being tied to my system account, all gone. Now I can understand the fingerprint reader login option being reset, but I had to re-enroll my fingerprints as well.
(I'm still going back and trying to get everything set back up again, so I don't know about the Windows Store apps, yet.)
So if you should have the need to do a "Refresh" on Windows 8.1, make sure your preferences are all backed up.