I was thinking something along the lines of:
Got rare mission A. If mission A is not completed, you've got random events B and C as well as mission D showing up. If mission A is completed, it also disables prematurely, before they would have a chance to show up B, C and D. Of course, if we'd want to go extra ambitious, we could even add completely branching paths. If mission A is complete, events/missions B, C and D get disabled but another mission E is enabled. Etc etc
Generally, it's all like the idea in the first post: "If rare mission is not stumbled upon or lost, allow some 'another chance' missions, or alternative consequence missions and events to show up later. If the player manages to do it, don't enable or disable those 'you've got another chance' missions/events".
Examples already provided for stuff like Morozova or spider queen. Probably many more could be made. Hell, I can think of and probably could write you mock up texts for many events (by 'events' I mean those popup messages describing random stuff happening, often affecting council's score) that could show up or be unavailable depending on successes in various missions, story developments etc but that's slowly moving away from the main point of this idea and even more of work for you to add them in and I don't know if you'd be interested in such.