Cheers for that info on the .fusehidden files. I don't have many books on my Kindle, I delete as I read them (on the Kindle itself), and generally add books using Calibre. It's not jailbroken, it's always ejected safely, but I've had one or two of those .fusehidden files (plus some part download files, can't remember the specific name) and wondered what they were.
I wouldn't touch any files outside the documents folder, but anything in it that isn't a book file have been deleted, and so far my Kindle still works just fine.....