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

Easiest thing to do is just launch the GUI client of VirtualBox and remove (possibly after shutting down) the virtual machine. You can just right click the virtual machine and perform these actions.

The following bash function would poweroff and destroy all files related to all VMs for the current user:

function killvms() {
  VBoxManage list runningvms | awk '{print $2;}' | xargs -I vmid VBoxManage controlvm vmid poweroff
  VBoxManage list vms | awk '{print $2;}' | xargs -I vmid VBoxManage unregistervm --delete vmid
}

Add it to your ~/.bash_aliases and call it in your shell via killvms.