I am a little puzzled, when you say via ssh, you mean you are using a ssh connection to the vSphere servers to run the vmkfstool there?
When it fails, is the ssh connection closed ? or just the vmkfs command fails?
I had done that kind of clonning without troubles in the past, using a ssh connections and indeed a 2TB disks took almost a day, used screen from a server on the same LAN to run the ssh and it did not fail.
If you can live without having it thin provisioned, it is possible (and easier) to clone the disk directly from the vSphere client, just browse the datastore, right button copy, and then right button paste over the target folder.