Skyrim SE Plugin List

[Kaisenati]

But I reinstalled and I checked they ARE installed what the heck... There goes my save...

[7531Leonidas]

A lot of your problem seems to be that you do not really have a good concept of what file overwrites do in conflicts.  Vortex automates the overwrite process, using its built-in LOOT to assume a proper arrangement of load order for your mod lists, patches and all.  The cyclic rules can come from your choices during installation, or just internal conflicts between the information LOOT uses for different mod files.

You have to think through what the purpose of each file is, and which one(s) should be loaded last, in order to produce the result you want.  In the above, CBBE is the base mod, the WACCF patch and the Dawnguard Armor and Weapons files have to load in an order that allows them to make their changes to that base file.  Check the WACCF mod page for suggestions on where to place the CBBE patch, if it is to be loaded before CBBE, then your diagram shows that that is the case.  If the opposite is true, then flip that rule, and that rule only.  If the WACCF CBBE patch is properly ordered, then you will have to flip the rule between it and the Dawnguard Armor and Weapons, since both build or add to CBBE.  The 'cycle' is that arrangement of overwrite arrows making a nice little race track that flows around the triangle.  When you get more complex cycles, you can right click (I think) on an arrow to highlight the cycle that it is a part of.

WRT the missing stuff, I can't really help, reinstalling may have changed choices in the FOMOD for LUX.  Why did you reinstall, instead of checking the 350+ conflicting files, and choosing overwrites individually to resolve your problem?  You could try to uninstall/reinstall again, but the Immersive Citizens patch should not be available, if you have disabled/removed Immersive Citizens.  You might also try loading the save anyway, then saving again, and finding out what happens.  What you have seen with the missing files is what happens when you remove/disable mods during a game, messy stuff happens, especially when you have to reinstall stuff to get it to work.

[Kaisenati]

It is interesting npcs I removed, not immersive citizens. I thought reinstalling would help I didn't know it wouldn't be there when in reality it is and should be. I didn't know what to do with checking the 350+ conflicting files list. When I try to load that save it CTDs so it's no good.

[7531Leonidas]

Yeah, it's a lot to take in - you have to click on the specific line that states how many files are conflicting in that mod.  From my LO, see the 27 files line, I clicked on it and got the following:

The 2nd pic shows what happens after you click the 'Edit Individual Files' button.

3rd pic shows what is seen when I click on the 1st line, see the two choices?  The top line is the current 'winner', simply click (or double-click? - I didn't try to change anything at all, so not sure) on the other to select it as the new 'winner'.  Read the dialog at the bottom of the 2nd pic to see what Vortex says about the process.  This may not help you until you get things sorted out, or give up and rebuild everything, but at least you will have some idea of how to pick apart some conflicts.  You can still go to your mods page, and see what the conflict bolt for Lux gives you, you don't have to change anything right now, just look and see.