Reconciling Story vs. History

When writing any kind of story, publishers and agents expect a tight plot where every word counts and every plot point has a reason. My book doesn't quite do this, and the reason is that in my novel I am writing not just a fantasy story but also a history. Sure, it is fantasy, so I should just be able to change any detail I like, because I created it, right? Not really. This story existed in my head for so long - more than twenty years- that it has essentially become historical fact within my created world.

This is a problem, because history doesn't tie things up nicely the way publishers and agents want stories to be. I have an almost war between the races of elf and man, halted due to the threat of a far more dangerous invasion from out of the East. I imagine many agents would tell me to ditch the whole approach to a war that never takes place. It's boring, because there is only a threat of action, no true action. To me, the threatened war between elf and man is something that actually happened, so I can't just cut it out. I imagine my created world as a real place with a real history, and history muddies up tight stories. I like it that way; it feels more realistic to me. Life doesn't work in neat, logical plot points.