I've seen it happen in all sorts of stories. They separate the buddies. Kirk and Spock, Richard and Kahlan, Han and Chewbacca, Alec and Seregil - the magic is in their relationship, their banter, they way they save each other's lives. So when you separate them, often the story loses a little interest for me.
Now there's always going to be the secret quest, or a kidnapping here and there to spice things up. But I think it's very important to bring the characters back together as soon as possible. I'm working through that now. It made sense to separate them at the time, but now I see I've fallen into that same old trap. I need to get them back together pronto.