Refcache files are data to optimize xEdit's loading speed the next time you try to open the same file, this is not a file for the game, Don't clean Fallout 3 and New Vegas DLCs, due to engine bugs and the bugs in the ESMs themselves it will cause issues in game.
Change Filter() function in the "Apply custom scripted filter.pas"
function Filter(e: IInterface): Boolean;
begin
Result := not SameText( GetFileName(WinningOverride(e)) , 'Plugin.esp' );
end;
Change with your plugin's name, it also should be loaded last.
Unless Sheson modified something in DynDoLOD, the lodgen's nif textures gathering code is single threaded. It is for sure in lodgen's on Nexus and people report corrupted nifs using MO there. So I'm 99% sure the reason is MO, just not in your particular case.
There is a sudden increase of reports about corrupted nifs (and even corrupted lodsettings(!) files) in lodgen nexus comments too, and we are talking about lodgen versions which have not been updated for like 2 years and always worked perfectly. Considering that all reports come from MO users and they happen randomly, I'm 99% sure this is a concurrency MO bug in it's recent versions.
I think the problem here is your lighting mod and harsh normals on LOD meshes which make it more apparent. Spherical normals bending on leaves will probably help a bit.
Update to the latest version, 4.0.2 as of now. Make sure to have Edit Scripts folder installed together with FO3Edit.exe because worldspace browser is a hotkeyed script.
There have been a lot of changes in modgroups recently to discuss all of that here. Join the xEdit discord, the button is in the top right corner of xEdit window in the latest github builds.