The mods should still be there. CHeck the data folder. I use NMM which sets the load order file (hidden) to read only. I also use the Nexus FO4 launcher. WAYYYY better than the original.
It also sets the ini files to read only when you exit it. For those who are having issues make sure the /meshes, /textures, etc stuffis still in the fallout4prefs.ini file.
It can reset becuase of the prefs file located in the main FO4 directory. That is used to create the one located in the saves directory.
I do use 1.2.37.0 though so Im opting into the beta. ALthough I opted into the previous patch and I dont remember my mods being disabled.