Good news! My wife’s permanent residency has been approved. Well, they still have to do the final assessment by an immigration officer, but it’s basically been approved.
We need to respond to their email, then print out our reply and the attached file to send to the Manila office. After that, they review it and let us know when landing is possible. As far as I know, my wife can either exit the country and return, or go to the immigration office downtown and officially land.