You can put this check app state logic in a separate workflow and your other remaining logic in another.
Invoke both workflow from Parallel activity and check mark the Isolated property of both.
You can increase the wait time of Check App state to approx. time your code requires to run.
With this approach your both workflows will work simultaneously. Check app state will keep looking for the popup and as soon as it finds, will click on Continue. Also your main business logic will not be interrupted by it.
Thanks,
Ashok 