I lost all my apps in my itunes library

I had been having a problem with my iPhone4s and Itunes communicating. Every time I attached my iPhone iTunes would report an error that the Library could not be updated.
I followed instructions on how to more the .XML file, restart iTunes then reimport the library. The problem is that now NONE of the Apps I had are there, and if I attach my iPhone it wants to delete the apps on the phone and replace it with the ones in the iTunes Library, which at this point is only two!
Help! How do I get the apps on my iPhone BACK into my iTunes library!
Thanks in advance,
Lee

Al lpurchased items can be found by clicking Store > Check for available downloads

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