Moved library and lost iOS application files

I moved my iTunes libraries using iTunes 10. Using the "change file location" function and the "Organize Library" function. I needed to move them out of my user folders to a more central location accessible by all users.
I had to do it in two steps because I have 50GB of media but didn't have an extra 50GB of space on my macbook drive. So I moved it once to an external firewire drive. Then deleted the files off my main drive to free up the space. Then I moved them back to my macbook drive, again using the built in iTunes functionality.
Everything worked fine for my music and movies and video. But my applications didn't move. And now I am not sure how to fix it.
When I select Applications on the left in iTunes 10, it shows the icons of all the applications I have - but there is a little exclamation point on each icon that indicates iTunes can't actually find the files. If I click on an icon it wants me to locate the files - but I don't actually have them any more.
I have synced my iPhones with no problems, all the apps are still on the iphones.
My problem is I just upgraded an iPod touch to 4.1 and I need to update all of it's apps but since iTunes can't find any of the files, it won't update them on the iPod.
I have 130 applications purchased with three separate Apple Accounts, and installed on two iPhones and one iPod Touch. There is a bug (already logged and accepted) in the iOS that it won't let you update all your apps on an iDevice if they were purchased with separate accounts - it gets into a goofy "validate account" loop that never gets resolved. So the only option until that bug is fixed is to update them using iTunes on my macbook - then when you sync the iDevice they get the updated applications.
It looks like my only solution may be to go and "buy" each app (download) again individually - but that will be extremely tedious, and a pain for me to remember which account purchased which app... And for 130 apps, having to "search", and "find", and "buy" each one and having to do it logging out and in to each itunes account will be annoying.
Does anyone have any suggestions? I wish there was a "re-download apps" functionality in iTunes.
Thanks if anyone has any ideas...

I have an idea. not sure how well it work.
I've noticed that when I connect my phone to a different
computer is tells me I have apps on the phone that are not
in itunes, and would I like to copy them into itunes.
so here is my idea.
quit itunes
rename the itunes folder
start itunes - it will create a new itunes folder
plug in your iphone, hope it asks you if you'd like to copy apps into itunes
(don't sync your phone else you might lose everything on it)
If this works, it should generate a folder called Mobile Applications.
Copy this folder into your old renamed itunes folder.
Delete the temporary itunes folder, rename the old one back, and all should be well. Maybe.
I wouldn't do this without having a good backup, and I also wouldn't do it without first looking carefully to see if you can find your existing Mobile Applications folder.

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