zilav

Update script a bit, find this part
if HasCheckMasters(sl) then AddMessage(Name(e) + ' \ ' + Name(el)); and replace with
if HasCheckMasters(sl) then begin AddMessage(Name(e) + ' \ ' + Name(el)); MarkModifiedRecursive(e); end; It will mark found records as modified aka bold font in the left records tree.

https://github.com/TES5Edit/TES5Edit/releases

formids := ElementByName(formList, 'FormIDs');
SetEditValue( ElementAssign(formids, HighInteger, nil, False), Name(weapon) );
 

The advanced filtering method is a scripted filter. Apply this script https://pastebin.com/raw/nnJUvpU9

Assigned() returns a boolean value. Scripts try to convert all values to strings when you print them, however you really should work with it as bool
if Assigned(_aidt) then AddMessage('Element exists'); Also RNAM is not a name, it is a signature. If you are accessing elements by signature then use ElementBySignature. Or just always use ElementByPath which works with both.

Assigned() returns a boolean value. Scripts try to convert all values to strings when you print them, however you really should work with it as bool
if Assigned(_aidt) then AddMessage('Element exists'); Also RNAM is not a name, it is a signature. If you are accessing elements by signature then use ElementBySignature. Or just always use ElementByPath which works with both.

Right click on array's header in a plugin ("FormIDs" row in your case) -> Add

Right click on array's header in a plugin ("FormIDs" row in your case) -> Add

All form versions are supported and safe to use, been so since Fallout 3 back in 2008 when they added it.
Resaving plugins in CK before release is a good modding practice to fix whatever issues the official editor won't like just in case.

You need to use modgroups feature
https://www.reddit.com/r/skyrimmods/comments/3ejcfx/tes5edit_modgroups_advice_and_examples/

Do you use the latest build? Ignore version numbers, check the actual date on Nexus and on your current exe.

1. Weather mods and ENBs affect tree LOD colors, billboards for LOD are usually made with vanilla lighting in mind.
2. Tree LODs are flat images grabbed from a single angle, they don't have direction.
 
Both your issues are limitations of Skyrim's engine. They can be overcomed using ultra trees option in DynDoLOD, however it requires lod models for trees and there are none for SFO.

While TES5LODGen is a renamed TES5Edit, there is still a minor difference between them. When you launch TES5LODGen, it shows you the list of all worldspaces from all loaded mods, while TES5Edit will show worldspaces only from a mod you right clicked on. If there are no worldspaces that fit for LOD generation, the window will not even open in TES5Edit. Worldspaces "fit" for generation are the ones that have exising lodsettings file which is usually packed in BSA archives. Since MO with turned on BSA management hides them from other application except for itself and the game, xEdit/xLODGen can't access lodsetting files and won't work.
You either need to disable BSA management in MO, don't use MO or unpack archives.

While TES5LODGen is a renamed TES5Edit, there is still a minor difference between them. When you launch TES5LODGen, it shows you the list of all worldspaces from all loaded mods, while TES5Edit will show worldspaces only from a mod you right clicked on. If there are no worldspaces that fit for LOD generation, the window will not even open in TES5Edit. Worldspaces "fit" for generation are the ones that have exising lodsettings file which is usually packed in BSA archives. Since MO with turned on BSA management hides them from other application except for itself and the game, xEdit/xLODGen can't access lodsetting files and won't work.
You either need to disable BSA management in MO, don't use MO or unpack archives.

Nope, it is a faulty nif mesh from one of your mods. I asked Sheson to show mesh name when exception occures, but looks like he forgot to add that. You can try disabling mods to find out the source of issue.

The chances for cleaning to affect anything in game are very low for any mod. They could be only caused by bugs in the current version of xEdit, and I don't know of any atm.

Did you install NMC texture fix from FNVLODGen optional downloads? There is a broken lod texture for dark red cliffs included in NMC pack.