Updating OS... What to do with apps.

Do I somehow have to backup my apps when I upgrade my OS? If so how would I do that?

Just hook the iPad to your computer and just follow the directions in iTunes. Your app will be backed up, you won't lose them.

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    Were the apps on your computer's iTunes when you started the update process ?
    As long as the apps are still available in the store, and you use the same iTunes account as you originally used to buy them, then you should be able to re-download them for free : http://support.apple.com/kb/HT2519 . If you download them to your computer's iTunes you could then try restoring to your backup and see if that restores them and their settings/content - a backup doesn't contain the actual apps, just their content/settings, so for the restore to work fully iTunes needs access to the apps so that it can restore them.

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