I've read that you must disable mods that add their own DistantLOD objects before running the utility. (Knights of the Nine Revelation is such a mod.)
However, if I deactivate it, It also deactivates my bashed patch (and all the mods merged with it) because I assume that esp is a master for the bashed patch, therefore keeping TES4Lodgen from looking at those when it runs.
What is the best practice for getting around this problem?