When trying to create linked clones you end up with an error "object has already been deleted...".
The Parent VM is present on virtualization platform, it is shutdown and the snapshot has been created properly.
This can be caused when the Parent VM is in Independent Mode.
Open the parent VM's settings and uncheck "Independent Mode" for Hard Disk.
Recreate a snapshot and perform cloning operation again.
Independent Mode VMs does not include disks into snapshots.