CC doesn't have any mechanism to delete book files without also deleting the book in the CC database.
I suspect that the Amazon reader app is moving the books, especially if the books are purchased from Amazon and still have DRM. If the delete happens all the time then you can check this by reading the book, "doing something else", then checking if the book file is still there using a file manager.
It is also possible that the reader app is renaming the books. You can check this the same way: look in the "books" folder to see if there are files that you didn't put there.
If you
send me a CC debug log I might be able to provide more clues.