I just did an upgrade from Windows 8 Pro to Windows 8.1 Pro. I should have been suspicious when the options offered only included files & settings, but not apps. All of them are now in windows.old Office 2013, Visual Studio 2013, and everything else. That sucks that I wasn't warned.
Microsoft says:
"Your files, desktop apps, user accounts, and settings come with you. "
and
"We'll check your desktop apps and devices for you. As part of the update, we check your current desktop apps and connected devices, and let you know what you'll need to do to get them ready for the update,
or to get them working again after the update. "
I attempted the upgrade on my desktop PC. The upgrade failed for unknown reasons, but I'm glad it did. At least I can try to find out how to save my apps before losing them.
Regards,
-Robert