Hi,
Did you try to use Wait for window content or Wait for image action after the first action is : Open an application?
From my point, when you have your first action is "Open an application" and right after that you can have another action that "Wait for window" or "Wait for image", so with these actions you can recognize that the popup appears from the other application so that you can click OK button from there.
That was my thoughts.
Hope it can help you.
Mike
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