All downloaded applications disappeared during Sync

I sync my iPhone to iTunes every day. I have had the phone for a little over a month now with no problems. Today I plugged it in, synced as usual, but when the sync was done, ALL of my downloaded applications are gone, both from my phone and from the Application tab of iTunes.
The Application link under Library in iTunes still shows all of the applications, but when I plug my iPhone in, the Applications tab there is blank.
The apps do still exist in My Documents\My Music\iTunes\Mobile Applications
I have deauthorized my computer, and reauthorized it. I have shut down iTunes and restarted. I turned my phone off and back on. What else can I try to get my applications back?

OK, I did an 'Add Folder to Library' and selected the Mobile Applications folder. The applications now show up again in the Device list, I clicked Sync, and the got copied back to my iPhone. Whew.
But now I have TWO of everything in the Applications section of the Library. There is only one physical copy in the Mobile Applications folder. I shut down iTunes again and restarted. The duplicates are still there. I tried Consolidating the library. Nope. Preferences hide the Applications folder, then unhide it. Nope, still there.
I am now going through the applications one by one, double-clicking on them, and doing a right-click Delete of the ones where the associated file can't be found. iTunes definitely lost track of the applications when I moved My Documents.

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