This happened to me on one of mine this past weekend. I use the atv flash with boxee, but must have not turned off auto-update on the latest flash. So after the update everything was gone.
I tried doing a restore and behold it was back to ver. 2.02 where I bought the atv. I then did the atv flash update and boxee was back.
I know this is a work around and I probably loose something, but to be honest I haven't noticed much in any of these updates since I primarily use the atv to access stored movies and TV on my Drobo.