You made sure that the permissions were set correctly right (rw-r-r)? You may also have to clear your cache, because if it has the old libraries cached then it would try to load those cached libraries instead of making a new cache with the new libraries, causing it to freak out when trying to boot upWhen I switched out the stage fright files and checked it came back as immune but the first time the phone rebooted It hung at the boot loader.I Had to dirty flash the rom to get it working again.
I didn't see this because I always tend to clear the cache when I make any system changes, plus I also used GravityBox's Soft Reboot a few times too, I think Xposed has a Soft Reboot option as well in the Installer APK