in situation 1, you have to remove the cloud.uuid from the VMX file before issuing a delete. try testing that on a trial VM.
I'm pretty sure you can clone the VM in vCenter, remove from inventory, delete the VMX entry, then register back to inventory. I'd also suggest a Display Name and Folder Name (on the datastore change) at the same time before registering back into vCenter inventory ... that'll help differentiate it from all the other vCloud VMs.