Each case is dealt with individually. As far as the situation with baptismal certificates in the province of Quebec goes, shortly after September 11, 2001, the then Minister of Citizenship and Immigration and Quebec Minister Facal made a joint announcement concerning which Quebec documents would be accepted as official documents. It was announced that only documents issued after January 1, 1994, by the directeur de l'état civil would be accepted for a citizenship application.
On June 5th, 2007. See this statement in context.