Isso foi explicado na série limitada de quadrinhos da Babylon 5, "In Valen's Name", escrita por JMS (e Peter David), de modo definitivamente canônico.
Delenn reveals that after the last Shadow War, Babylon 4 was taken to a place of rest, its final location a secret. The crew who took it there never returned. Its fate was a mystery for nine hundred years -- until now.
Não consigo encontrar minha cópia da série, mas eis o que uma wiki de fã da B5 diz sobre a conclusão:
For over 900 years the station lay dormant, guarded by the Tak'cha, who referred to it as Ende X'Ton ("the lost station") which they believed to be a holy place. In 2261 it was found floating adrift in Sector 730 by 12 by 9 by John Sheridan, Delenn, Michael Garibaldi, and Susan Ivanova. Within 48 hours of rediscovering the station, Babylon 4 burned up in the atmosphere of the planet it was orbiting.