A character comes back to life?

I would have included SPOILERS alert but it's unlikely anyone will ever see this movie. If anyone else had seen this movie they probably would have already posted this thread's topic.

So here's what happens: Abernathy(?) is killed in his office by Jolly Roger, and Jolly Roger makes a joke. Abernathy's sorta hot secretary is jamming to her headphones while this happens. As Jolly Roger leaves Abernathy's office he sees the secretary jamming and gets very angry. Her eyes don't glow, so we know she is not a necessary person for JR to kill, but he seems to be annoyed by her jamming. So Jolly Roger winds up a big swing of his sword and we see him aim right for her head as the song she is listening to (we can sorta hear it a bit) gets to a scream and she screams(because of the music).

This is actually one of the best off-screen kills I've ever scene. EVER! It's beautifully choreographed and very creative.

But then when the police arrive and find Abernathy dead, the secretary runs into the scene crying about finding her boss dead. Wasn't she just killed? Did the actress playing the secretary forget that her character was dead and run onto the set while filming? And the director said, "let's leave it in, it'll give the movie some LOSTish mysteriousness."

I still can't figure out if I'm missing something, maybe the DVD has more footage that explains what happened? I'm baffled.