first get the world id - login to esxi ssh console and run cmd:
esxcli vm process list
You get a list e.g.:
ws3 World ID: 387290 Process ID: 0 VMX Cartel ID: 387289 UUID: 42 0c 0d 6d 22 b9 83 73-46 d1 ee 14 13 09 82 06 Display Name: ws3 Config File: /vmfs/volumes/9e8fce4f-70868c6e/ws3/ws3.vmx
Then you can kill the process of this vm and unregister it:
esxcli vm process kill --type=force --world-id=387290
List of VMs:
vim-cmd vmsvc/getallvms
Kill:
esxcli vm process kill --type=force --world-id=2103017