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Basically, when you write a flow to the config datastore, if the switch is connected it gets pushed on the switch, then written on the operational datastore. If the switch goes down, operational datastore does reflect it, as you pointed out, by removing its entry. But the config store remain the same, as it's the config store, e.g. not supposed to reflect the operational state of the device, but the desired state. So when the device comes back up, the flows present in the config datastore will be submitted to the switch, and if success, will be written in the operational datastore.

So if you want the flow to be removed from the config datastore when the switch is doing down, you have to create and submit that transaction yourself.

Hope this helps, Alexis