Push notification when (for example) a door has been open for too long

Flows
2

As you said you need a delay that can be cancelled. There are many apps that can provide that functionality, my personal favorite is Chronograph - Adds precise timer, stopwatch and transition functionality to Homey. In the flow that is triggered by the opening of the door you can start a timer. Another flow needs to be triggered by: a timer has ended, that will send the notification. And a third flow will be needed: if the door closes: stop the timer.