You proably put the download and/or mod-staging directory inside Vortex' own installation directory. This is *NOT* the default. You had to put it there yourself, so there's noone else to be blamed for this than you. As a matter of fact there are multiple warnings here in the forum, NOT to put ANY data inside Vortex' installation directory. And, I'm sorry, but there's no way to recover your mods. They're still injected in your games, but you cannot deactivate or uninstall them anymore. So best is to start from scratch and follow the best practices this time (i.e. using the default installation directory in c:\Program Files, and either leave the downloads and mod staging folder at their default - if your games are installed on C: as well - or use some custom location OUTSIDE of Vortex' installation).