I don't know what LOOT is, but I am having the SAME EXACT problem with MO. I uninstalled and reinstalled Skyrim SE and I now have a completely, pristine Data folder and I even uninstalled all of my mods in MO and reinstalled some of them. At some point, MO stopped working. I started to notice that some mods which I was installing didn't appear to be showing up at all. And, if I uninstalled an older mod and reinstalled it, MO would not recognize it. I later uninstalled and reinstalled MO to see if that would help, and it did not. Whenever I try to start a new game, it continues to tell me that the .esm and .esp files are missing. I check the mod folders and find that they are there. That's when I started to back up my Data folder, I tried to make a pristine one, but it continued to make the same error. I later uninstalled and reinstalled Skyrim SE, which took HOURS, and it was the same problem. I later deleted all of my mods in the Mods folder of my MO AppData directory. And, the problem continued to persist. One odd thing to note is that I have an alternate song, and that is still playing whenever I start the game with MO. It no longer does this with Steam Skyrim SE as I uninstalled everything and cleared it out. However, Alternate Start doesn't load, and I think that that's because it was one of the mods that I uninstalled and reinstalled to see what the effects would be. So, my guess is that something somewhere outside of the Skyrim SE folder and the MO's AppData folder is causing this problem. Perhaps a file in the Program Files (x86) folder of MO? I tried researching this on their wiki page, but I could not find anything like this in their troubleshooting section. This seems to be an entirely unique situation. This LOOT problem is the closest to my problem that I could find after days of researching. I seriously love using MO, by the way. The virtual folder idea is just genius, and it allows me so much freedom when it comes to trying out various mods. If the annoying black face problem reemerges, then I don't have to uninstall everything, but instead, one-at-a-time, unclick a checkbox and click back again to pinpoint which mods are conflicting with which. The ease of installing and uninstalling mods is so awesome, that I don't want to go back to Nexus right now. HOWEVER, it's not loading my mods and I don't know why. Please help me.