Well, the simplest approach could be to generate and store the hash of some files, then have the "watchdog" to repeat the hash and compare it against the stored list.
Here, you don't have a live protection, but at least you may be confident that your backup doesn't copy malaware-encrypted files.
No doubt that searching the Internet will lead to some available tool. But if you can write your own, it will be a lot more difficult for pirates to break it (since thay won't have a clue on your design specs).