If you accidentally deleted your Vagrant directory, and you have an orphaned VM sitting in VirtualBox, you can re-associate it with a new VagrantFile. Here's how.
When new VM is first created for a given VagrantFile, Vagrant creates a .vagrant file in the same directory. It contains a JSON array, which stores the Unique ID:
You need to re-create this file.
1) Determine the Unique ID for the VM.
To see a list of all Virtual Box vms:
$ VBoxManage list vms
2) Re-create the .vagrant file by adding the appropriate UUID to JSON a array in .vagrant.
3) Recreate the VagrantFile.