I'm not real sure what you're talking about here, but I've been having a problem that I think has to do with Vortex itself.
I had a set of mods I was using and was experimenting. Started having trouble, so I deleted all the mods, then uninstalled Vortex.

Then reinstalled it and, the mods I had deleted showed up. I was trying for a clean slate.
This must have to do with Vortex itself.