First thing your going to want to do is download and endorse FallrimTools
Extract the file somewhere and run Resaver.exe
You will get a window with your saves in it.
Select the latest one (Sort by Date Modified).
Now, select from the clean menu, Remove unattached instances (ctrl+1) and Remove undefined elements (ctrl+2)
Now in the top left box type "_ds_", this will show you all of hunterborn scripts. Right Click Scripts and then delete.
Save your game as a different name under File and Save As.
Load your game, open the console (~ key to the left of the 1 key).
Type "setstage ski_configmanagerinstance 1" and press enter.
All your MCM will now be rebuilt and your ready to go.