The original special effects for B5 were famously done on 'Video Toaster' technology used on the old Commodore Amiga computers, right? Did they ever get around to updating it to more regular PCs later on? Changing to a completely different computer system might have contributed to those earlier FX shots no longer being available. As well as the fact that the commercial life of the Amiga itself died sometime around 1994. Could the Amiga files have been migrated to a new operating system?
EDIT: Wikipedia tells me they stopped using the Amiga after the first season.