How do I destroy a VM when I deleted the .vagrant file?

The following VirtualBox commands might help. If poweroff doesn’t work, try unregistervm.

$ VBoxManage list runningvms
$ VBoxManage controlvm <uuid> poweroff
$ VBoxManage unregistervm <uuid>

Source: https://support.cloud.engineyard.com/entries/21449637-I-deleted-Vagrantfile-vagrant-and-or-the-app-directory-before-halting-the-VM-Now-ey-local-up-errors-

Shell script to stop all running vms:

VBoxManage list runningvms | awk '{print $2;}' | xargs -I vmid VBoxManage controlvm vmid poweroff