It is also normal for the X to chow on the apps, but when you click on them they should be redownloaded from the app store.
The app store is rebuilt, so those 3rd party apps are missing from the registry but are still installed, thats why they still show up. Then after the repair when you go to click on them windows will download anything missing info it needs from them, a lot of times going to the app store and having it check for updates will do the trick as well. I even had it auto doit after a few reboots as Windows keeps the app store up to date automatically.
Shane