Vortex uses shared downloads (archives) and mod staging folders (installed mods) for all profiles for a game, currently. This means that when you change a mod version in one profile, that change would be reflected in other profiles as well.
@Forestwolf17 To answer your question - Removing a mod would remove it from both profiles, not just the active one.
It would be a great update to Vortex if they could add a feature to make a separate staging folder so that if a profile uses a different version of a mod, it would install that version to a staging folder only for the selected profile, rather than all profiles.
For example, if you were managing Fallout 4 and wanted to have a profile for old-gen and one for Next-gen, this would not really be possible with the current functioning because the staging folders are not separated. That use case is not practical anyway, but illustrates the point.