Six year old install broken upon update attempt

[AffordableSolarguy]

Running about 400-500 mods, for years now, my Fallout 4 install is very old,, 6-8 years old, I have very slow internet, takes several days to install. So, I tried to clean it as loot kept recommending but it did not, instead led me to update, and that failed .  I then opened Mod Organizer 2 and all my manually installed mods ore gone.  A bit stressful.  No clue what happened. 

[lmstearn]

With installs that old, best to hold everything in the time capsule, suspending all updates, or completely reinstall - in which case starting a new game is recommended.