Activating mods and irreversible changes in Documents folder with Vortex

[WastelandProject]

I'm trying to activate some mods that were disabled after the last patch of the game. F4SE is updated, the game works but when I try to activate some mod with Vortex (enabling it) strangely that enabling involves permanent changes in the folder
 game in documents. What happens is that the game doesn't start (immediate CTD of the launcher) and even disabling the mod via Vortex doesn't solve the problem, everything has changed in that folder and you need to recreate the files via Steam to make the game work again.