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Why can't I see my apps in itunes on the left side? While at the bottom in the summary it shows I have 147 apps?
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I've never been entirely sure whether app data is reliably backed up by iTunes. In reality, many apps have their own backup systems, usually by finding a backup option in the app itself.
Personally I rely on the app itself. If memory serves me well, when I last changed my phone, as soon as I signed into my account with the app, all my data appeared.