Can you not just take the NTFS drive out of the Windows machine temporarily and plug it into the hybrid? This would, by far, be the fastest way of doing it.
If so, unshare the Windows folder and turn off the Windows machine
In the web admin, in Media Sync turn on the missing files check box
Delete the entire folder structure that contained the media on the Windows machine.
Put the drive into the hybrid - note you can actually do this whilst the machine is on if it is SATA as SATA is hotplugable
Tell LMCE not to use the drive.
Now use either the command line or KDE desktop to transfer all the media to the correct hybrid drive location
After a while, UpdateMedia will scan in this media
Transfer the drive back to the Windows system.
Remember to clean up LMCE by deleting the share "device" in the admin site