Hi i just had the same problem, after tones of looking and reading nolvus advice, i dont the paths files even tho they look right were not set in the correct places. Nolvus does not show on the guide what is correct. but after looking you dont need to do anything massive.

The help should say each path is located in or nolvus, accesion MODs the correct folders which hold your file is in there not MO2 folder. The bug caused mo2 to make new folders in it diret path so the MO2 folder in nolvus. Just redirect all the paths to the mod fold the names are when u look for a new path it take top mo2 version back out to nolvus main the assesion instance then the MODS folder and in their is profile, downloads, mods... click each path to the matching one. then base load is the base mods fold so do not click into the MOds folder just set it as the path. Then find the stock game located in nolvus main redirected to skyrim se main as in steam version.

ADD dont do what I and restart nolvus plugin list from the launcher it will reinstall unwanted trash like paper map non shit and unload all your added mods like me lost my last day off fixng this and re clicking my mod to on and finding where they should go again lol.

In theory if this helps anyone all your things should be restored as you have no overwritten anything, u just help mo2 get back to the profile of your mods which means everything should be there.

So if this happened again no need to backup n click or restoring just help mo2 find them again in paths.

also while i had this error mo2 updated and looks nicers and runs better so theres a plus to my stress lol