Installed Mods Showing as Not Installed, and Causing Problems when Reinstalled

[deasthope]

I have a LOT of mods installed (198 active, but stable), and have had a weird problem plaguing me for a few weeks: a large portion of my mod list is actually active - there are loaded plug-ins and meshes/textures appear in-game - but in Vortex, they appear as if they have never been installed. The game is still stable and all the content is there, but Vortex doesn't seem to have the mods "attached". Deployment works just fine, and I can even add mods that overwrite others and it properly detects the conflict and asks me to choose which one should take priority. No issues selecting overrides or moving things around in the "web" view (when there are multiple conflicts to resolve), but in the master list, a huge portion (probably about 30%) all appear with the "Never Installed" button.

 

 

 

Now here's the weirdness. The other day I noticed that a single texture, which I know is installed/touched by a mod, wasn't appearing. So I went to reinstall the mod. It was one of the "Never Installed" (but actually loaded) ones. When I clicked the button to install, it asked me to reinstall or create a version, and I asked it to reinstall over top; it did so. Then, the conflict resolver came to life, and asked me to pick either the mod, or the exact same mod; despite detecting the overwrite on installation, it still thinks there are two instances of the mod.

 

Is there anything I can do? I know Vortex uses a JSON file to organize its stuff; is there any tinkering I can do in there to make it identify the installed-but-not-recognized mods?

[HadToRegister]

Well, you could rename the file and have Vortex re-create the file