When I had this issue I moved the entire MO2 directory out of the common folder and into the Skyrim directory, which is where we are used to having it. Since it is on the same drive it will be an instant move. After that ZEdit was able to read my load order...FNIS wouldnt work for me till I did that as well...try this but on an individual basis for each section. Move it, build the patch, move the folder back out to the common folder When I was done with the entire guide I made the choice to leave the entire MO2 folder in the skyrim directory as a flavor choice but it is recommended to leave it outside the skyrim directory and in the common directory.