It's my understanding that personal data on the iPhone 6 is automatically encrypted with the user's passcode. This is why when you boot it for the first time the passcode is required instead of the fingerprint.

My question, however, is why after the first boot, before entering the passcode for the first time, does the iPhone continue to receive account-specific notifications? As an example, Google Hangouts will actively receives messages that are readable and on the lock screen before any decryption has taken place. Wouldn't this imply that the user data for apps somehow are not encrypted?

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Probably because you didn't just reboot it. All you did was turn on the screen.

Once you enter the passcode, some but not all of the data remains accessible until you turn the phone (not just the screen) off. To turn the phone off, press and hold the power button for 5 seconds until a "Slide to turn off" slider appears, and slide it.

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