I'm scrolling through the list, and I'm not seeing it. I'm trying to get Tsugumi's final weapon, and I can't do it without that boss's analysis. Am I going to have to play through Yuito's story again? I don't even remember that being a proper fight. I seem to remember Kasane interrupting it, and I don't recall getting any analysis for it.

It isn't. Some bosses like Naomi Randall and Court Mort aren't in the vision simulator. If you don't have the analysis from the boss fight, then you might've inadvertently traded it for a gift exchange token.