You don't necessarily need to remove/add the VM from/to the inventory, reloading from the command line will do too (see http://kb.vmware.com/kb/1026043)
I'm not 100% sure with using PowerCLI to modify the .vmx file, but I think since this is done through the API you don't need to explicitly reload the configuration. Search Google for site:communities.vmware.com lucd modify vmx and you will find a lot of samples.
A couple of settings can be modified using the VM's Advanced settings in the vSphere Client.
André