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Member Since: Mar 04, 2008
Posts: 1,115
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Mac Specs: Unibody MacBook Pro 2.26, 4gb RAM, 500gb HD

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This warning is referring to your iTunes Library on your HD. (the collection of iTunes data stored on your HD--not the wooden bookshelf) You have purchased (or downloaded for free) one or more apps directly from the App Store onto your iPad. iTunes is asking to transfer a backup copy of these newly downloaded apps onto your HD. You should always allow this transfer to take place. This is an integral part of syncing the iPad to the MBP.

In the unlikely event that your iPad died, was stolen, etc. You can get a new iPad, plug it into iTunes, click restore, and iTunes will restore the new iPad to the condition of the old one. Transferring a copy of all apps to iTunes is also a requirement to restore the iPad after updating the firmware.
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