As far as I understand it, this only applies to applications from the Philippines from May 31st 2015 under phase 3 of the UKVI Biometric Residence Permit – International Rollout Schedule

Spurs, are you stating that this new BRP protocol was applied to your wife's application and subsequent granting of her visa ?
Did your wife have the new 30 Day travel vignette in her passport ?

If there was no travel vignette and no approval letter from UKVI then it has not yet been applied.

Please let us all know the status for your wife's passport vignette.