What I did:
I often duplicate an event in Fantastical, because I’ll be working on the same task multiple times.
What happens:
The linked note in Agenda then automatically moves to the date for the last instance of that duplicated event.
What I would expect:
That the linked note is still assigned to the date of the first / upcoming instance of the duplicated event – it seems logical to not do anything to the linked note if the original event still exists?
Alas, this is not something we can’t control, because when you duplicate the note Fantastical or the Calendar app will also duplicate the link in the note field of that event. Which means Agenda sees this as the link to the event and updates the linked note. The solution would be to during duplication, clear that agenda URL from the notes of the duplicated event.
Aha. Well, at least we have a workaround 
Cheers!
A
I use a similar, but somewhat different technique: I set a reminder for an item in an Agenda note, and then manage it with BusyCal. It allows me to schedule long tasks (such as writing a paper) spanning through multiple days:
I’ve been doing this for many months now, and it’s very efficient. I have a problem similar to @ahnissen 's, though, because I want to check each instance done, even though the full task is not completed (therefore, I want to keep it unchecked in the originating note in the Agenda).
The technique actually worked best in the past before synchronization was fully implemented in the Agenda.
I think the desired feature would be to have an option in the “edit reminder” window to switch on/off synchronization with Reminders for the given task (perhaps located just below the calendar selection).
Why this feature is interesting? Because I can schedule when to start a long task directly from inside the Agenda. I would later do the duplications in BusyCal (e. g. when planning my week). I have even created a KM macro to make this more practical:
The workaround is nice, but it would be better to keep the link in the many instances of the tasks in BusyCal, and use it to locate the originating note in the Agenda (e. g. for marking the task done when it actually ends).
Thanks for the example, need to think how it would work exactly. My feel is that de-coupling from reminders is not the way to go, but perhaps there’s an alternative way.
Thank you, Alexander. I guess the “switch on” option might produce inconsistent situations. Another idea could be to only mark the item as done in the Agenda when all instances of tasks in Reminders are done.
I’m curious - is BusyCal somehow displaying the same task (“Aritgo Natorp”) on 3 different days? How does that work?
I simply duplicate the task (⌘D), sometimes spreading instances (copies) through the day, sometimes duplicating a task for the next day or for many days in a row. For the latter cases, I use the Keyboard Maestro macro above (⌥⌘D).
I also check each item done when I finish working on the long task for the day/period.