I don't quite understand this, if you have Samba you can access the NTFS partition to read files and transfer them straight to the PC, but how do they get there from the Sky Box in the first place, didn't think the Ellion could write to NTFS.
Incidentally you can also access the UDF partition file that the ellion writes to when recording if you are using Samba. This might be an answer to your problem.
I think it's somewhere around about /usr/local/etc/hdd/dvdvr/DVD_RTAV or somesuch so you probably need to configure the directory in smb conf as well as setting it as a network place on the pc.
You may be able to edit the smb conf file directly if you have a text editor which will not mess with the file's line ends (I use pspad).
So long as you do each recording and transfer individually, removing each from the record index after copying it should be straightforward. If not, your transfers will be very slow. I think my record file is 30 gig for example.
hope some of this helps. There is info on how to configure samba in a number of places both on this board and others.