Studio One does have an issue with refreshing the plugins list properly if you have updated or removed something.

This is the only workaround that works for me:

1. Make sure you close Studio One.
2. Go to %AppData%\PreSonus\Studio One 4\x64
3. Delete the Vstplugins.settings file. DO NOT DELETE ANY OTHER FILES!
4. Relaunch Studio One.

The plugins list will then be rescanned and refreshed properly. The plugins you have uninstalled will no longer appear in the list and those updated should be working again.

By doing so you will not lose your custom settings you might already have in place for various plugins. At least for me, this procedure has proved to be harmless. I would nonetheless advise that you think twice and make a backup of any settings or anything you deem precious before proceeding. I think it should be perfectly safe but I still have no idea what it might do to your specific setup. Don't kill me if there happens to be some specific problem I didn't know of. I'm trying to help.

Note: If you prefer to turn off rescanning the plugins at every startup, then you will need to turn it back off (because deleting of the Vstplugins.settings file will change that setting back to default): Options --> Locations --> VST Plug-Ins --> Untick Scan at startup --> Apply.