> How do you protect yourself against incomplete writes?

I don't update files on disk in-place. I write to a new file, and once it's done I do an atomic move and replace the old file with the new one.

> What about when there's a critical update that you don't want lost?

I immediately write it to the disk? (:

I don't think it's possible to completely avoid this problem. In a traditional database if you suddenly lose power you'll also lose that critical update, if it hasn't been yet committed to the disk.