I really don't know if there is a connection between relationship break-ups and nightmares... I believe the article I read had to do with grieving in general, and the loss of love aspect was thrown in. But, from what you say above, it would make sense, since the person is somehow in your subconscious thoughts, if only because they are no longer around and so routines change, etc...
Am always fascinated by the fact that schizophrenics, other delusional people, are often inspired by their dreams, (see colors and shapes, connections between words, more vividly for instance) and seem to be able to set them down on paper via some artistic endeavour, often in a more dramatic way than the rest of us. Why is that?
Just out of general curiosity, how do you know all this about the brain's workings?