Why did a whole bunch of apps disappear from my iPhone!?

A great many apps, a number which I cannot guess, have suddenly disappeared from my iPhone upon sync with the new iTunes 9. After this sync, I installed iPhoneOS 3.1 and sync'd again. The apps are simply gone. They're not in my trash bin. They're not in my Home Directory. They are still in my Home Directory under ~/Music/iTunesLibrary/Mobile Applications
Why have they disappeared from my iTunes Library? Why did I see a message stating they were being removed from my iPhone? What gives? Some of my most used applications were simply removed without my permission.
What happened to the Apple Macintosh "It Just Works" slogan? Apple's software of late has not done what I want, and tries to think on its own. Stop that! Do what I say. When I click, you jump. When I don't click, don't jump.

I just experienced this same **** problem! I synced my iphone with my computer (like normal), i noticed it was taking a while to sync so I canceled it only to find that ALL OF MY APPS ARE GONE! I'm glad i stopped it because it started to delete my music. and even the folder that I had associated with my itunes library is not showing up in itunes. It surely is an itunes problem, not an iphone problem. I am aware that I can re-download them one by one for free but I want them all back with out hours of doing that! they are even gone from my applications file in iTunes. I'm with you in that apple really has abandoned that whole, "it just works". because it does not "just work". They try to use itunes to lock down their **** but it just turns out to be a pain. I want to know of a place in my account that I can simply go to download all my apps at once?! apple can be so smart sometimes, but so stupid other times and very user unfriendly with regards to the iphone. thumbs down apple.

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