I am dumping NMM for my SSE and going to the newly updated MO. I had seen the SEPTIM guide earlier and thought it would be a nice stable playthrough base. As its a fresh start of sorts I decided to get the folder move over with also. Never as easy as it reads I have gotten past all issues so far except one...I cant get LOOT to run properly through the MO inside my SSE install. It seemms to see the base game contents but none of the mods already added to my new MO install. I am assuming its a pathing issue for LOOT but where do I repoint it to see my MO mods folder or wherever it needs to see....
Thanks for reading.
I run all my games on a separate SSD, Skyrim included. One thing that helped me with stuff like loot, script / save cleaners, etc. is installing them right into the Steam/steamapps/common/Skyrim Special Edition directory, where the game is located. Also, set up their respective repositories, archives, etc. right in the Data folder.
I'm not sure how this will or will not affect running it from within MO, but you can try. Basically install Loot and any other external utils into Skyrim directory, start each manually 1st, go to their settings options and set up their respective paths, sometimes you'll need to manually create a folder in the Data dir, once you do all this, then start MO and link / input paths for the utilities etc.
May want to install MO in the same way as well.
Please also beware, that there was a Microsoft bug which I came across and had to deal with, which has not much to do with Skyrim or the individual programs. Basically, in Windows 10 ( I forgot which builds / patches were affected ) the operating system had trouble or did not properly recognize and process applications installed on a separate SSD or M.2 drive, other then C:\ or drive other where the main Windows operating system resided. Regular HDs were not affected. This has been patched by Microsoft but fairly recently (within last few monthly updates), so depending on your OS, its build, version (patches) and your installation choices for Skyrim and its corresponding apps / utilities, you may be affected by it.
Once I got the patch from MS, my issues went away and have been resolved.
So if you're on Win 10, make sure its up to date, and install all the applicable stuff into same drive or same folder. This might help you out. Though of course there may be other stuff going on, but I think its worth a try. And use something like Ccleaner in between installs / re-installs to get rid of any invalid path and registry entries.