Some of you may realize some of this stuff, but I didn't really think about it until I got bitten.
I wanted all my books - Amazon and non-Amazon - to show up in the "Books" tab, so I had been copying them into my Books folder on the Fire.
The first inconvenient thing about this is that if you have already used the Kindle reading app since you last rebooted your Fire, you'll need to reboot your Fire (or just kill the Kindle app, which is a lot quicker!) to get new books to show up in your bookshelf.
The next inconvenient thing about this is that the books are not stored in the cloud. Which leads to the most inconvenient thing...
I de-registered my device (trying to solve an unrelated problem of my own creation) and did not expect what happened: almost ALL the contents of the Books folder were deleted, not just Amazon books. The only thing NOT deleted were a couple folders I had copied over in early attempts to sideload non-Amazon books (I just copied the whole folders from Calibre and then realized the Fire doesn't look in them, but never deleted them).
I still had the files on my computer, so the only big deal about this is having to re-locate my reading position, but still, a surprise.
So I guess going forward I will email (non-DRM) books to my
me@kindle.com address. Sure, they will be in Docs instead of Books (which I don't like just because they're books, darn it!) but they'll be stored for me in the cloud.
If you use a 3rd party reader... don't save your books in the Books folder!