I thought I was having a similar issue but found the cause for me. First the way I fix it is by going into Alfred's Advanced tab and clicked "Clear Cache" all my missing apps are then found.
The reason this happened to me is because I use MacCleanse. It's default cache cleaning mode includes the System - User Cache data. When this is cleared Alfred still seems to find files but Applications completely disappear until I go and manually click "Clear Cache" for some reason using the "Reload Alfred Cache" keyword command doesn't fix this. It's only when I go in and click the "Clear Cache" button.
Hopefully this helps.