ALL apps deleted from iPhone and iTunes after newest iTunes download

ALL of my boyfriend's apps were deleted from his iPhone 3G AND iTunes after he downloaded the newest version of iTunes onto his PC. Does anyone know why this happened? Can he get all of those apps back somehow?
Thanks!

The only way all iTunes content on his iPhone can be removed is if he synced his iPhone with iTunes after the current iTunes version was installed and his iTunes library on his computer is now empty. A warning message should have been provided indicating this would happen if he proceeded with the sync.
His iTunes library on his computer is now completely empty - no music or anything else?
Nothing available in the iTunes named folder located in his Music folder?

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