Hello there,
1. When you remove a vmdk you get two options.
Remove the hard disk from virtual machine: this detaches the vmdk from the respective vm. However the vmdk is still present in the VMs datastore
Remove the hard disk and delete files: this Removes the vmdk from the vm as well as delete the file from the datastore. All data in that disk is lost.
2. Svmotion is the correct procedure to rename vm files once the virtual machine is renamed
3. Sysprep is used for guest customization. Without guest customization the SID of the deployed VM from clone or template will be the same which causes isses.
I believe if you are running Windows 2008 and above then there is no need to create a sysprep file as they are include in the guest OS.
Suhas