It *should* have saved your recording gracefully before shutting down. If you are running on external power, it won't save anything when your power is cut.
2 hours does seem short, usually I can count on at least 2.5 hours per battery. Unless your battery is older you should be getting the same runtimes. Of course, everyone's case is different.
Poke around in the archive and also the rest of the Remote Power threads and you'll find some thrifty ways of providing cheap reliable power to your JB3.
Good Luck to you...