One change that has been noted by those who neglected to disable auto-updates when they installed Boxee, is that the update unceremoniously removes the third-party add-on.
Not only does the Apple TV update process not give any update as to what's included in the update - it's turned on by default. If you don't wish to disable your Apple TV's third party add-ons you should turn off auto-updating. Like now.
Update: A post on XMBC.org details how to turn of Apple TV's auto update feature:
1) Open terminal 2) type: ssh frontrow@AppleTV.local 3) type password: frontrow 4) type: sudo bash -c 'echo "127.0.0.1 mesu.apple.com" >> /etc/hosts' 5) close terminal
Why does Apple do stupid things like this? Pressure from the networks, perhaps?