When cloning a running VM and choosing Customize Virtual Hardware, there is a major problem. The only change I am making is to change the NIC Portgroup. But instead of only changing the portgroup, it also changes the drive backing of all the hard disks to point to the original VM's .vmdk files. With the original VM running, you can not power on the new VM due to the locks on the files. If you have powered off the original before powering on the clone, then you can be royally messed up. The drives are being cloned and are in the clones folder, but once the file copies are complete, the new VM is being modified. In the event viewer of the cloned VM there is a huge entry where it is changing the drive config as well as several other settings.
For full disclosure, I am cloning a VM with multiple hard disks between two different clusters with different distributed switches and VLANs. So it is necessary to change the port group. We are cloning VMs between test and production clusters. This is fully repeatable on every VM that we have tested so it is not a configuration or environmental problem. It is bug.
I do understand that the Customize Virtual hardware option is and has been forever marked as "Experimental", but this is an expected use of the option that should work. The program should only be changing those options that are modified in the wizard, it should not be changing anything else. This is not an acceptable situation. I have used this wizard for years to add drives, change CPU and Memory settings and it has always worked fine until now.