Hey did you find a solution for this. Tried Bethini for the first time today and had the same issue. Tried reinstalling/uninstalling the map mods I have but no luck. Also tried to move the mod to load early as suggested but did not work as well. I use Dyndolod so maybe I'll have to regen the textures and LOD? Seems weird that I have to do that to fix a map bug though.
In Skyrim Special Edition, this file would be CreationKit.ini under your installation folder, the default being C:\Program Files (x86)\Steam\steamapps\common\Skyrim Special Edition.