Amazon will not disturb your non-Amazon files, nor will updates mess with them. I have books from all over the place, only about 1/4 are from Amazon. While the nature of Amazon's system allows them to "see" what's on your Kindle, it really just looks at ID numbers (called ASINs, similar to ISBN numbers) so that it can update and sync content you buy from them. It doesn't disable or disturb the other books, and if a book doesn't have an Amazon ASIN number, their "spy system" probably doesn't even know what it is. You'll be fine with non-Amazon books.
"The crap is legion." - MrsJoseph