I usually only put the edge of the flashlight beam on the owl at night and then I manually focus the camera if there isn't enough light to autofocus.
Another trick I have used for mammals at night is a laser pointer with some sort of filter on it - the kind of "toy" gadgets you can get that project shapes, etc..
If you can get one that projects an image of a tic-tac-toe board (straight lines at 90° to each other), your camera can lock focus on that from a great distance in otherwise total dark. Just be sure not to point it at the animal's head - point at the branch below it.
The laser pointer is a great idea. To solve the problem with focusing over a great distance I've been using a spotlight. This doesn't give me a lot of time before the animal is scared off by the bright light. A laser is much more convienient and discrete.
This is why I love these kinds of discusions. Tricky photograph situations yield a lot of inovative thinking and it's so interesting to hear about all the solutions people find.
I'm going owling very soon, hopefully I will have some pictures to show!