EDIT: This was in the iPod and iTunes section... but you're talking about App Store apps for an iPhone or iPod touch, correct, and not the old iPod games? I'll move it to App Store based on that assumption. If you're talking about iPod games, I have no idea and apologize.
When I tried to move my iTunes library from one computer to another, the same thing happened -- everything was recognized except the apps, which appeared in iTunes (for me) but were not usable / uploadable to the iPhone.
Options:
- The ones already on your device will sync back to iTunes.
- You don't have to pay for anything again, but if you can't get your computer to recognize the copies it has, you can go to the App Store, and attempt to re-purchase all the apps you had. When you attempt to purchase it again, you will get a dialog stating that you already bought it and will be offered the option to download it again for free.
Sorry, don't know a better way.