Just to ask a question: Vortex asks to you, after deploy, to confirm external changes and you press save changes? I ask this because I'm experiencing a similar situation, but I'm figuring out to solve it case for case. It seems that when Vortex asks to confirm external changes it's going to delete all the previous mod files you installed and if you select "revert changes" it doesn't touch anything and some mods will work. I said SOME mods because I noticed that: - The mods made to work in the mods directory will work - The mods made to work in other directory won't work until you manually deploy them following the instructions from nexusmod post Said this I'll open a post apart asking if this is a feature and/or if this is related, could be, to the deployed mode (I'm using the default mode that is simlink mode).