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What kind of software upgrade are you talking about? Once you jailbreak, you don't want to allow iTunes to update your phone. If necessary, there are ways to reinstall a default firmware, and the Apple Store geniuses would have no way to know it was jailbroken.

If your son was savvy enough to jailbreak, he should be able to read the sites and forums that are teeming with helpful instructions to recover from almost all errors.