Actually, this is a very important feature of good EV/EVO mission writing. Here are some examples
Cycling missions:
You have a mission which becomes available at a particular moment in the plot. You want the player to do it at least once before he or she goes on to the next. After that, the player might want to do it again for financial reasons.
Multi-thread rejoin:
Your player can take either route or both routes to a certain point. Each thread ends with the mission bit being set, allowing the player on to the next section.
Excluding another path:
There are a variety of choices which prevent a player from going down one path (eg, joining the pirates, fusion-bombing a developing world, joining the guerillas). Each one of them sets a bit which is required not to be set for the path you are excluding. It doesn't really matter how many of the bad things they do, as long as they do one. You might think that you could accomplish this with legal status, but in fact the player can quite easily up his or her status by fighting the pirate fleets that follow him or her into systems if he or she has escorts.
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