Bethesda has officially rolled out patch 1.2, and it's in full gear on Steam. However, it also came with a new launcher that breaks mod support, according to Nexus Mods.
On the bright side, user Gameaholic posted a solution on the forum thread. Before getting started, though, you're going to need the Nexus Mod Manager.
Once you've got everything you need, here are the steps to fix the problem:
1. Open the Nexus Mod Manager, initially enabling the mods.
2. Launch Fallout 4, but don't hit that Play button just yet!
3. Re-enable the mods via the Nexus Mod Manager, which were disabled when the game was launched.
4. Hit the Play button.
5. Fasten your seat belts, play the game and watch as Bethesda loses the fight.
It's unclear whether or not Bethesda intentionally removed mod support. After all, the game developer is known to support mods and the modding community.
Some fans speculate that Bethesda did this intentionally to get players to wait for an official mod workshop, whereas some say that it's merely a bug. At any rate, the workaround is effective, it's here to stay, and we can continue on with our mods for now.
It's also worth mentioning that the Fallout 4 Script Extender has been updated to be compatible with the latest patch, but the tool still relies on the Nexus Mod Manager to work.
And of course, let's not forget the changes that the patch brought. The update added in two new features: number pad keys can now be used for remapping, and Remapping Activate now works on Quick Container.
It also came with a couple of tweaks here and there, including fixes for the player getting stuck in terminals, equipped weapons becoming locked after completing Reunions, the quest "When Freedom Calls" would not be completed, the continuous health drain during "Confidence Man," the game crashing for jumping into water and reloading saved games and the Launcher not saving God Rays Quality setting properly.