Bureau 13 was dropped (as a name) because of the the existing game. The Psi-Corps woman was dropped because she was tied to Talia's story, and when Andrea left, there was no where to go with that. She wasn't someone who could later be connected to Lyta without it seeming contrived.
In story terms it is assumed that the group known as Bureau 13 changed its name. This happens all the time in the real world of covert intelligence, especially if a codename somehow becomes public. Even large organizations get their names changed - the Soviet security service was variously known as OGPU, NKVD, MVD and various other high-value Scrabble words before settling on KGB.
The mere fact that we don't see something twice doesn't make it a loose end. There were entire stories going on (the Mars resistance, underground opposition to Clarke on Earth, events on the outer colonies) that only caught glimpses of, or only heard about, because they weren't part of the main B5 story as seen from the perspective of the folks based on the station. Even if Talia had stayed we probably would never have gone back to San Diego. Her future confrontation(s) with Abby would likely have taken place on B5 or on Mars. San Diego was just used as a location for that base because (a) it was cool, and referred back to something already established in the B5 future history and (b) an abandoned, radioactive city is the ideal place for a covert base. Who is going to go looking for you there, or even consider it as a possible location?