I have the exact same issue. Game is installed on D Drive, .esps are in my game data directory, but no mods are showing up in-game and the Add-on list is blank. Edit: Nevermind, just fixed it. Hopefully this solution works for you guys as well: Navigate to C:\Users\[username]\AppData\Local\Fallout4 In my case, Plugins.txt was set to Read Only and was not populated with the mods in Loadorder.txt. By disabling the read-only, copying and pasting the contents of the mods in loadorder.txt, saving and setting Plugins.txt back to read-only, I was able to restore my mod functionality in all respects.