Hmm, I've never had silence where the battlefanfare theme is supposed to be.
My guess is that if it doesn't see a song to play there, it'll still stop the battle theme and just play nothing. You could try individually editing the scripts for each battle, to have them not stop the currently playing song, the way they do in a few places (bombing mission comes to mind).
edit: Fixed. I meant the right thing, just had a bit of a brain fart when typing it.