No, this isn't referenced elsewhere.
When Captain Sheridan takes command of Babylon 5 in Points of Departure, Ivanova mentions that she served with him on the transfer point off Io. When Garibaldi comes out of his coma in Revelations, he specifically states that he doesn't know Sheridan and doesn't trust him.
Franklin gets no such character beat. Franklin discusses the new captain with the others at the end of Points of Departure, which gives the impression they might not know each other, but little else. The first time Sheridan and Franklin are shown on screen together (and might, in theory, have just met) is when Franklin discusses Garibaldi's treatment with Sheridan in Revelations. They keep it snappy, but there's no indication for or against Sheridan and Franklin working together before.
The one item that is referenced is the circumstances that led to Franklin being roped into the mission. He was asked to turn over medical information on the Minbari for bioweapons purposes and refused, which led to him being arrested first, and then roped into the peace mission later. His refusal is discussed with Delenn in Season 1's And The Sky Full Of Stars, but not the mission stemming from it.
We can take from this a slight in-universe assumption that once the mission was over, Sheridan and Franklin simply didn't know each other that well outside one failed mission and were probably ordered to keep it classified regardless.
As for the mission's notability - well, as Londo relates in In The Beginning, both Earth and Minbar assumed that someone from their own side was responsible for the attack. Neither side would have liked to talk about that kind of betrayal from within, doubly so for the Minbari, to whom killing their own is unthinkable. If it was investigated, starting from that assumption, neither side would have gotten anywhere close to the truth. Safe to say that someone in Earthdome said "we tried", swept it all under the rug, and moved on; as important a mission as it was, two more years of all out war and later epic events (The Line, the attempts to build the Babylon stations) would have eclipsed a brief meeting in an old bunker in history and memory anyway.
As @Rand pointed out in comment, the writer J. Michael Straczynski has gone on record in response to a fan comment to a very similar prompt. It seems they were intended to know each other, but nothing much about it made it into the show proper.
Yeah, in my notes on Sheridan I had him meeting Sheridan before, but never did much with it at the time...we never see the first time Sheridan and Franklin meet in the second season, and when we do they're hanging out pretty casually, as people who've met each other before might. Bear in mind, also, that there's about 11 years between the two incidents, and at best they were casual acquaintances on one mission.