Apps from iPhone to iTunes

Once upon a time - I had itunes setup so that I could transfer any downloaded apps that were on my phone to itunes. But ever since I formatted my PC and installed a fresh copy - itunes just wants to delete my apps, so now I have no back up if say ALL of my apps suddenly want to stop working like they did today.
Now wouldn't be such a big deal if all my apps were just fine and dandy but since I have apps that were pulled from the store like "Tris", I cannot get that back if I delete it.
So is there anyway of getting my apps to back up to itunes? Its extraordinary that this isn't possible that I can tell. I just want my TRIS!
Spanks a lot.

To anyone that can help me:
I recently upgraded my iphone software and when I go to access my apps and associated data, I find the icons on the phone are merely pictures and when I select the icon it tries to load, unsucessfully, and immediately returns to the home screen. I can not find any of the data files on itunes, nor can I open the apps on Itunes, though again there are just icons of the apps under the "Applications" tabs.
I am a musician and had original compositions saved in iTalk.
Thanking you in advance!

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