So, yes the game did get updated and I needed to wait for F4SE to get a new update to match so I could try again. While waiting, I decided to fire up skyrim and play that. After several hours getting my setup going and running smoothly THE EXACT SAME THING HAPPENED. Now, the 60 mods that I am running in Skyrim suddenly stopped working to include, once again, the simple texture replacers as well. Clearly this is not a problem with updates or mismatched files but with MOD Organizer 2 and I am at the point of tearing my hair out here. Skyrim worked fine for about 10 hours and after restarting my computer for the night it hard broke again. Something is causing me to lose all my mods and I cannot, for the life of me, figure out what the hell is going on. Even uninstalling and reinstalling them did nothing.