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I started the upgrade from Windows 7 ultimate to Windows 8 Pro. The first time I ran it I had all three "Choose what to keep" options. I chose "Nothing" and hit next. After a second I decided I wanted to keep all so I just canceled out of the window. When I restarted the Windows 8 setup I can not get the option to keep my apps to show up. Any ideas?

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You could try downloading the windows 8 upgrade assistant again. –  Jay Oct 27 '12 at 20:50

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Happened to me as well. I fixed it by deleting %LocalAppData%\Microsoft\WebSetup (i.e. C:\Users\UserName\AppData\Local\Microsoft\WebSetup) which the Upgrade Assistant creates every time it is run.

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