I installed Windows 8.1 from within Window 8 and noticed my apps don't work anymore, some are gone and a ton of stuff is missing. Is there no way to keep all the Windows settings and apps when doing this upgrade?
Upgrading to Windows 8.1 from windows 8 without losing apps is possible. There are two things to note here 1) The installation language must match your system's default UI language and 2) a specific Windows 8 edition can only be upgraded to its equivalent or higher edition.
For example, if you have Windows 8 Pro English-GB installed, then you can only upgrade to Windows 8.1 Pro English-GB or Windows 8.1 Enterprise English-GB without compromising application data.
I found this information at this link and it worked for me.