I may have figured out a solution after reading this pointer. By passing an empty string, the API appears to randomly generate its own instanceUuid. I used the following and it seemed to generate a new vc.uuid:
$spec=New-ObjectVMware.Vim.VirtualMachineConfigSpec
$spec.instanceUuid = ''
$vm=Get-VM-Name$vmName
$vm.Extensiondata.ReconfigVM_Task($spec)
