Each firmware update from Apple will normally erase non-Apple menu items from AppleTV.
Boxee users simply need to re-apply the patchstick to add the menu item back. Additionally boxee software and data persists so after the patchstick has be applied, user logins, media sources, preferences, etc. will be just as they were before the upgrade.
Calm down and carry on,
Andrew & Team boxee
Patchstick Link: http://code.google.com/p/atvusb-creator/