This was explained in the Babylon 5 comic book limited series "In Valen's Name", written by JMS (and Peter David) so definitely canon.
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.
I can't find my copy of the series but here's what a B5 fan wiki says about the conclusion:
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.