Looks like you already figured it out, though I hope this'll be helpful to others:
Most of the files generated by the editor (story.div, goals.div, goals.raw, story_ac.dat, ...) are completely useless and are not loaded by the game. They're intermediate files that are not supposed to be packaged at all. (I believe the latest DE editor fixes this issue?)
story.div.osi is the story file compiled from the mod and its direct dependencies. As long as the list of loaded mods and the list of mod dependencies matches, the game loads story.div.osi directly. If there is a mismatch, it'll take all goal files (found in RawFiles) from all mods, merges them into one single story script file, and compiles that file.
In practice, this means that if you use more than one mod it'll almost always trigger a story merge, so you don't have to update story.div.osi at all.