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Disappearing buildings

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The only mod I see that you have that has been known to cause this issue is "Scrap Everything".

I used to use this mod.  I would delete vanilla buildings in settlements and then rebuild form one of the settlement mods such as "Homemaker".

Taffington Boathouse was an example where I would just delete the house and start over.  The problem is you break "Precombines".  

This is where Bethesda combined several things together for efficiency like maybe a building, a tree, and a car.  If you delete one object the others are still there but you have broken part of the precombined meshes.  PRECOMBINES AN IMPORTANT THING TO KNOW AND WHY YOU SHOULD CARE : Fallout4ModsXB1 (reddit.com)  


Sometimes a mod will also cause this if it is also editing the Precombines.  Mods that update Goodneighbor, Diamond City for example can cause flickering of meshes like buildings or your character can fall through meshes.  Precombines can be repaired when a mod is created but I have seen mods cause issues with this.


Anyway your likely issue is your scrap mod.  You would probably need to go back to a save where you did not have this mod installed.  You may not see issues at first until later in the game.  Some people say they have never had this issue, but I have and had read up on it in some mod guides.



Side note.  You can use zEdit to merge your plugins.  You have a lot of mods that are easy pickings for this.   zEdit is the successor to Merge Plugins.  It is not totally finished but the merge part is functional.  I usually merge the patches that belong with a mod for a start.  Why have 4 ESP plugins, with 3 being patches and 1 the main, when you can have just one.  Some Mod Managers allow you to hide the plugins of the original mod.  You can do this and active the merged plugin.  If something strange happens in your game just deactivate the merge and unhide the formally hidden plugins.   Follower mods don't always like to be merged for example.

Clothing and weapon mods are another good candidate.  Be careful of merging mods with dependencies unless you know how to use Creation Kit or XEdit to change the master dependency.  zEdit is available here:   Releases · z-edit/zedit · GitHub





Edited by Samuraitech
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