When you inject FBI there's an option to delete of keep the installation files so maybe you picked the option to delete them instead of keeping them, so when you went to install to sysnand right after then they weren't there anymore.
Unless there was some time between you installing it to sysnand and installing it to emunand and you are 100% certain the files are there.
Also if you're going from emunand 4.4 to 10.3 you'll have to re-inject FBI as it will replace the H&S app with a newer one