I actually have both lenses (that is the 100-400 and the 400 5.6), and use them both quite a bit. It comes down to what I am photographing at the time. If it's birds, then usually I will have the prime, either on the 1D or the 7D. Mainly because I am usually far away and am going to crop anyway, so the zoom is irrelevant.
For just about anything else though, I really like the versatility of a zoom. At a race for instance, I can zoom in on the action and bring it out wider as the cars get closer. Same thing at a wildlife park or zoo.
I would have a hard time deciding which one to give up if I had too. I have many keepers from both. First world problem, I know.
