Ok, let's say we have an event called after ND at day >=3. Then we run a second event at day >= 6, and it is a continuation of the first event.
Now, if player was inside SE for a week and returned at the 7th day, the events still will work, but one right after another, without a pause which is supposed to be there according to the concept.
You're supposed to use quests system for that... series of events make a quests and even lets say that you don't, you never setup events like that when you need second event to happen 3 or more days after the first one, you create first event to happen at >=3 and at the end of that event register a new event (second one) with the game to run on: >= day + 3.
I also don't get wtf day >= 3 and day >= 6 are supposed to mean in the first place if they don't literally mean: day >= 3 and day >= 6 conditions are acceptable to you, basically you're saying that any day higher than 2 is right for the first event and any day higher than day 5 is right for the second event so yeah, if they happen one after the other on day 7, it's exactly what you told the game to do... if it was:
1) day == 3
2) 1 has happened flag + day >= 6
I'd understand... you miss the event on day 3 and you're done with this chain. I also recall quests system having a progression where event 2 will not happen before you complete event 1 but I am not sure if I ever actually used that option.
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It's not possible to write "perfect" events/quests system where we assume that events can do anything, even if you returned from ND to main screen on day 3, it is not guaranteed that your event will be executed if some event with higher priority is scheduled and that even may ruin it for you as well (by for example forcing next day to occur).
I guess it's about coding/debugging your code and let people test, trying to understand what issues there are and adjusting for them, like with any other code.