The CGI files weren't lost until after Crusade went out of production. Up until that time, Netter Digital had the CGI files, which were legally the property of Warner Bros.
B5 decided to bring the effects in-house after S3, at a time when Foundation Imaging had fallen on hard times and begun to lay off workers. (Many of whom were hired by the Babylonian CG production team, which eventually became Netter Digital. Foundation's fortunes turned around not long afterwards when they got the contract for Voyager. By contract Foundation had to turn over to Warner Bros. all of their CGI models and files, and these passed to Netter. Later when Cruade folded everything again went to Warner Bros., which lost it all sometime between the summer of 1999 and the start of production for Rangers.)
Netter Digital wasn't organized as a company until well into the shooting of S4 and doesn't appear in the credits until "The Illusion of Truth". Various software packages were used for model building, textures, lighting and animation at different times under both companies. (Not to mention different hardware platforms ranging from Amigas to Wintel PCs.)