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There are a couple of ways to rename a Virtual Machine, but there are two in my opinion that stand out:

1. Shutdown the VM
2. Rename the VM in VirtualCenter
3. Migrate the VM and move it to another Datastore
4. done!

And from the service console:

1. vmware-cmd -s unregister /vmfs/volumes/datastore/vm/vmold.vmx
2. mv /vmfs/volumes/datastore/vm-old /vmfs/volumes/datastore/vm-new
3. cd /vmfs/volumes/datastore/vm-new
4. vmkfstools -E vm-old.vmdk vm-new.vmdk
5. find . -name ‘*.vmx*’ -print -exec sed -e ‘s/vm-old/vm-new/g’ {} ;
6. mv vm-old.vmx vm-new.vmx
   for every file that hasn’t been renamed (.vmsd etc.)
7. vmware-cmd -s register /vmfs/volumes/datastore/vm-new/vm-new.vmx
8. done!