Can you clarify your question? As you upgrade the iOS on your iPhone device, there is no additional steps required with regard to re-installing apps, or configuration.
JorgeM
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not upgrade, formatting
Ok, so I guess you what are referring to is restoring back to factory defaults...
When you have all sorts of issues with your iOS, you could invoke recovery mode to restore iPhone to default factory settings. this will restore the original state as when you first received the phone. The downside that all data and information stored on your phone will be lost. However, you could apply a restore from iTunes and that will bring back your data. I'd perform a backup before you invoke the recovery mode/restore.
You do have to reactivate after a clean, restore.
http://www.ehow.com/how_8299040_activate-iphone-4-after-restore.html
JorgeM
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