And don't forget... the apps in iTunes show under "Apps" in itunes "Library." Perhaps when you think you've lost your apps you are looking at iTunes Apps on "iPad"?? (And you can transfer purchased apps from the iPad to iTunes from the itunes File pulldown. It says "Transfer Purchases from [iPad]"
Also, if this is a new computer you'll have to re-download any app from the app store that is not "transferred" from the iPad.
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