The Shadows and Vorlons didn't really "make up". But their disagreement did become meaningless, and they were wise enough to realize it.
The entire source of the conflict was that they disagreed about how the younger races should be guided. At the Battle of Coriana, a fleet made up of all the younger races who were advanced enough to be relevant mutually
decided that they would no longer be guided by either side.
Even so, I think they would have simply destroyed the fleet and started over with a fresh crowd of faces if Lorien hadn't been there to convince them of the significance of the decision.
Sadly, Sheridan's "Get the hell out of our galaxy!" line weakens the entire thing, diverting attention from what's really going on at a crucial moment. But there's not much that can be done about that.