I can't seem to figure out why this isn't working. I disable all generated LOD before generating, I'm using the latest version of xLODGen, I build terrain meshes, I load this mod last and keep it enabled while generating, and I'm not using New Vegas Reloaded or ENB. Strangely, I seem to get the same problem without using any generated LOD at all. I've looked for any LOD meshes which might be affecting Zion, but there aren't any.
Opening this up in xEdit, I realized that Nevada Skies makes the same change to the water height, so the problem shouldn't have been there to begin with. Any ideas?
Alright, I managed to fix the problem. It wasn't an issue with the LOD, but with the standard Zion water. The RGB and fog values on the water made the LOD look extremely bright during the night, which made it look like there was a void, though there wasn't. I fixed it by copying the values from another water type over to the Zion water. It's not perfect, as the vanilla water wasn't perfect either, but it's much better.
Are you sure nothing is overwriting your lodgen output and that you had this mod loaded last in your load order while generating? You had the "build meshes" option checked as well right? Also are you using New Vegas Reloaded? With New Vegas Reloaded water LOD dissapears at certain view angles.
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Opening this up in xEdit, I realized that Nevada Skies makes the same change to the water height, so the problem shouldn't have been there to begin with. Any ideas?