The way I understand it is like this: You need the UK issued CNI in order to get a CNI from Philippines (you have 3 months to do this). After you have had the CNI exchanged for the Philippine one you no longer need the UK one, so it doesn't matter if the UK one expires before you marry. So yes, the Philippine one starts afresh.
Another peice of advice I'd like to give: Don't waste you precious time in the Philippines exchanging the CNI. Just post it there and you can get your fiancee (or in my case her family member) to do it for you. That way, theres less to do when you get there.
