I noticed, that texture swapped areas don't save their texture. So, when I swap the texture, save and reopen the map, the texture wouldn't be changed. I tried adding wmos and m2s to the map first, and then swap the texture. After I saved and reopened the map, the texture was gone, but the wmos and m2s are still there.
The log says:
[Error] Is "C:/Users/Bad/Desktop/Games/World of Warcraft/world/maps/azeroth/azeroth_38_26.adt" really a location I can write to? Saving failed.
I checked the folder, to see if the file exists (it does). It seems like noggit doesn't detect the file properly.