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I can't find any documentation for what happens with late/missed runs. Say for example a flow is scheduled for 1x per day at 9am and the system crashes. Eventually I get the machine and agent back online 3 days later. What happens to all the previously scheduled runs? 

The agent pulls all late runs and runs them by default when it comes back on.

Is there any config to only run the “latest” <@U01QEJ9PP53>  thank you. 

For Prefect Cloud we have <https://docs.prefect.io/orchestration/concepts/automations.html#automations|Automations> that let you cancel flows if they are late by X amount of time.

For Prefect Server, you have to do something more like <https://github.com/PrefectHQ/server/issues/307|this> where the run starts and then immediately cancels if it finds other copies of the flow already running