When you update a mod, the old version of the mod is Uninstalled. That is how it has always worked. The archive is still there, though, so you can rollback to an earlier version.
If you are making edits to mods, you should install them as a separate, customized mod in your mod list so that an update does not remove those customized files from the staging folder.
I have noticed that recently, Vortex does not always recognize a new version as the same mod. This can happen if the mod author changes the file name, but sometimes it happens even without that change.