I had a similiar problem when I just bought my new iPad and downloaded a ton load of apps to it.
iTunes saves the downloaded apps as .ipa files on your harddrive, and when I found them I just deleted them, and I've been synchronizing my iPad multiple times after, and havent lost any of my apps on the iPad.
The .ipa's is placed here if you're using windows:
C:\Users\<username>\Music\iTunes\iTunes Media\Mobile Applications
And here if you are using OS X:
User/Music/iTunes/Mobile Applications
Alternatively you can just do this:
For windows:
Open iTunes
Go to Library, and press Apps menu
Here you can see all your apps, right click just any if 'em
Press "Show in Windows Explore"
For OS X:
Open iTunes
Go to Library, and press Apps menu
Here you can see all your apps, right click just any if 'em
Click "Show in Finder"
Apple's Stackexchange site would probably work pretty well for this question, but this site fits the categories as well. – cutrightjm – 2012-04-10T02:37:30.723