Discrepancy

It just occurred to me those other copies of whruinstonedark.dds were meant to be transparent. Noble Skyrim 2k, CleverCharff's Windhelm 2k, and so on probably did this intentionally to get a more uniform look to the bridge, but for whatever reason the texture ended up all black on the atlas. I am guessing TexGen supports this if this file is made properly. I'll try one of the other files.

Thank you for that! I'm impressed you knew the exact texture. Of all the texture mods in my load order providing a version whruinbstonedark.dds, three of them were blank for some reason (including the conflict winner). I disabled all but one working texture, re-ran TexGen and the Atlas, and got no more black.I guess that partof the mesh just has a different texture for flavor. You must be right about the large reference issue - I do see that multiple copies of Windhelmbridge.nif are overlapping, base last changed by Better Dynamic Snow, which appears early and z-fights with the LOD. (This is only seen from a distance; I used tfc to get close and select it)

Thanks for this - I have it in my game too, and took the attached captures with and without tll. Confirmed no errors in TexGen_SSE_Log, and no mods overwriting TexGen output.