Sorry Mark, I don't understand your point or question
After the Naturalisation Ceremony did she then renew her passport? Sounds not. Means the Philippine Embassy are not aware she has British Citizenship.
Once someone takes the oath for British Citizenship then technically, and according to Philippine laws, that person automatically loses Philippine Citizenship until such time as they re-acquire it by taking the Philippine Oath.
Of course if that person never reveals the truth to Philippine authorities then nothing will happen until it is either revealed voluntarily or until it is somehow discovered.
Plenty of folks do that but there are some highly undesirable consequences.
Did your wife take an oath of allegience at the Philippine Embassy and receive a certificate of citizenship?