The way I've worked around this ever since I first had FO4 wipe my plugins.txt file clean is to make sure it is set to "Read Only' after making any changes with NMM, NMM unlocks the Read Only setting and then it seems FO4 launcher wipes the plugins.txt. Just get into the habit of re-locking it after any changes and FO4 will leave it alone until you use NMM to add/remove or move any Mods? Plugin.txt is in: Win 10: Local Disk (C:) Users > Your Profile > AppData > Local > Fallot4 > plugins.txt keep a shortcut of this Fallout4 folder on your desktop for quick access to the file, quicker than NMM, if FO4 does wipe the plugins.txt and you have problems with NMM there is normally a back up of the same esp details in the load order.txt saved in the same location You may need to set you PC to show hidden folders/files as some players used to have trouble finding the AppData Folder? PS: TBH Steam could not give a damn about passing down any Beth Updates that breaks players games, they changed the "Update when I say to" many years back to "Always Update" or "Update when I launch this game" they will not change it back. It stuffed up thousands of Skyrim players games and yet they still do it, only way to stop it is to stay offline with Steam, watch for updates, wait and see what the reports on it say, check for mod updates if needed, then go back online. Or be prepared to make a new start with every major FO4 update if it messes up any of the mods you use and breaks your saves, simple as that and they do not care.