How do I remove a Vagrant box from global-status, after deleting that box from the filesystem?

To discard old boxes listed in vagrant global-status (eg. you deleted the folder containing the .vagrant dir from the filesystem) you just need to run:

vagrant global-status --prune

You might need to remove the Virtual Machine directly from your provider (VMWare, Virtualbox, ..) control interface.

I believe that the new filename of the global data is ~/.vagrant.d.

So you can run rm -r ~/.vagrant.d to delete all user data for a fresh start.