Yes, for the VM's which don't require any snapshots, run "Delete All" from the snapshot manager to consolidate all snapshots.
For the VM's which require snapshots, you can only use vmkfstools for the base virtual disk. You cannot use vmkfstools to copy/clone snapshot .vmdk file without consolidating them. I can't tell you for sure whether the following procedure will work, but I think it should:
- remove the VM from the host's inventory
- clone the base virtual disk using vmkfstools
- use WinSCP and copy all files except for the flat.vmdk to the destination (overwriting the base disk's descriptor .vmdk file to maintain its original CID)
- rename the source folder (as a precaution)
- add the copied VM to the host's inventory
Since the .vmsn files contain metadata which may include the source datastore path and name, you may see this datastore name in the VM's Summary and I'm also not sure whether reverting to a snapshot will work, so you need to test this with one of the VMs.
André