I am having a similar problem. Edit: After checking all my mods against Nexus I noticed that quite a few of them showed a red bar on the files tab saying that no files existed. I am wondering if this is a Nexus problem, not Vortex. I don't really use Reddit, but I will try to find the support Reddit for Nexus. Edit #2: My bad I just realized that I'm not on Reddit. Doh!