I am having a similar issue. I did all the steps, and i realize how the folders work. And just to be sure, i've been rewatching tutorials and reading past forum posts about how to work with Vortex. But starting today, in Balder's Gate 3, half of my mods are no longer being deployed or recongized in game. I have about 150 hours in the game and this just happened out of nowhere. I have my Staging folder and my game directory installed on the same drive, yet is seems my main "Mod Folder" is now relocated in another path no longer inside my game directory. My Engine Injectors are working fine meanwhile normal mods are gone, even though they were fine before. Vortex also tells me they are properly installed. Deploying does nothing, neither does Purging. So i have some mods being deployed to my proper path and being seen ingame, but others are taking another path and not being seen ingame. I have no idea how to change my deploy path, or my main Mod Folder. I've been checking if it has anything to do with Profiles but so far i can find no fix for this problem. I am no where near being intelligent especially with Vortex, so any help would be appreciated.